Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Sedimentary architecture and evolution of a Quaternary sand-rich submarine fan in the South China Sea

Investigating the sedimentary architecture and evolution of sand-rich submarine fans is vital for comprehending deep-water sedimentary processes and enhancing the success rate of hydrocarbon resource exploration. Recent drilling activities in the Qiongdongnan Basin, northern South China Sea, have unveiled significant gas hydrate and shallow gas potential. However, exploration in this area faces substantial challenges due to the limited understanding of sandy reservoirs. Leveraging extensive newly acquired extensive 3D seismic data (~9000 km2) and well data, our study reveals five distinct deep-water depositional systems in the Quaternary Ledong Formation, including a submarine fan system, mass transport deposits, deepwater channel-levee systems, slope fans, and hemipelagic sediments. Notably, the targeted sand-rich submarine fan lies within the abyssal plain, situated at a water depth of 1300-1700 m. This fan exhibits a unique tongue-shape configuration and a SW-NE flow direction within the plane and spans an expansive area of ~2800 km2 with maximum length and width reaching 140 km and 35 km, respectively. Vertically, the fan comprises five stages of distributary channel-lobe complexes, progressing from Unit 1 to Unit 5. Their distribution ranges steadily increase from Unit 1 to Unit 3, followed by a rapid decrease from Unit 4 to Unit 5. Our results suggest that the occurrence and evolution of the submarine fan are primarily controlled by sea level fluctuation, confined geomorphology, and sediment supply. Specifically, sea level fluctuation and sediment supply influenced the occurrence of the submarine fan. Concurrently, the confined geomorphology in the abyssal plain provided accumulation space for sediments and shaped the fan into its distinct tongue-like form. In contrast to the deepwater channels within the deepwater channel-levee systems, the distributary turbidite channels within the submarine fan are marked by lower erosion depth with “U” shapes, greater channel width, and higher ratios of width to depth. The comparative analysis identifies turbidite channels as the focal points for offshore gas hydrate and shallow gas exploration in the Qiongdongnan Basin. Furthermore, the temporal evolution of submarine fan offers valuable insights into Quaternary deep-water sedimentary processes and hydrocarbon exploration within shallow strata of marginal ocean basins

Tectonic evolution and depositional response in southern continental marginal basins of South China Sea during period of rift-drift-foreland: A case study from the Liyue Basin

Based on the analysis of tectonics-stratigraphy-sedimentology in Liyue Basin, this paper finds out the characteristics of tectonic evolution and sedimentary fillings, reveals the genetic relationship between the basin evolution and the spreading of the South China Sea (SCS), and provides the reference for the study on the marginal sea evolution of the SCS.The Cenozoic tectonic-sedimentary evolution of the Liyue Basin could be divided into three distinct stages: the first stage characterized by continental marginal rifting and littoral-neritic clastic sedimentation from Paleocene to Early Oligocene, the second stage characterized by detaching-drifting and neritic carbonate sedimentation from Late Oligocene to Early Miocene, and the third stage featured with peripheral foreland flexure subsidence and regional differential sedimentation since Middle Miocene.In the first stage from Paleocene to Early Oligocene, the southeastward subduction of the Proto-South China Sea (PSCS) resulted in the passive rifting of the ancient South China Plate under the action of horizontal extension, and then the formation of the Liyue Rifting Basin.During this period dominated by the littoral-neritic depositional environment from Paleocene to Early Oligocene, controlled by detrital sediments supply and the PSCS action, a series of relatively large-scale braided river deltas developed in the northwestern basin, however, few small-scale fan deltas developed on the edge of the isolated uplifts in the eastern and southern basin adjacent to the PSCS.In the second stage from Late Oligocene to Early Miocene, accompanying with the PSCS continuous subduciton and the SCS initialization and spreading, the Liyue Basin located on the Liyue-Balawan Plate detached from the South China ancient continent, and then southwards drifted with slow subsidence and weak faulting.During this period dominated by the neritic- bathyal depositional environment from Late Oligocene-Early Miocene, due to the scarcely detrital sediment supply, large-scale carbonate platforms and reefs developed in the northern basin, while the bathyal environment was generally founded in the south.In the third stage since Middle Miocene, the process that the SCS spreading had being ceased and the Liyue-Balawan block was subducting towards Philippine island arc, led to the beginning of the evolution of the foreland basin in the Liyue Basin, characterized by asymmetric flexure subsidence, increasing water depth, and enhanced fault activity.During this period dominated by the bathyal- neritic depositional environment, it is the predominant feature that the carbonate platforms and reefs and deepwater gravity flow deposits have respectively being developed in the north and partial south of the Liyue Basin.It could be concluded that the tectonic-sedimentary evolution in Liyue Basin was closely related to the subduction-extinction of the PSCS and the spreading-closure of the SCS

Overpressure reservoirs of the Huangliu Formation of the Dongfang area, Yinggehai Basin, South China Sea

The relationship between reservoir property and such factors as sedimentary microfacies, clastic component, grain size, and special diagenetic environment of high temperature and overpressure were comprehensively analyzed to study reservoir characteristics and influencing factors in the first member of upper-Miocene Huangliu Formation of the DF13-1 structure in the Dongfang area, Central Diapir Zone of the Yinggehai Basin. The dominant reservoirs in the first member of the Huangliu Formation in the Dongfang area are composed of very fine to fine lithic quartz sandstones that are deposited in submarine fans sourced from the Kuntom Uplift. The reservoirs are characterized by large thickness, broad distribution and good qualities. High-temperature thermal fluids activities and overpressure are two major diagenetic factors contributing to the good properties in the reservoirs. Thermal fluids activities of high tempreture accelerated the organic matter thermal evolution and clay mineral transformation, and in this process organic acids and CO2 were generated which dissolved the reservoirs and thus resulted in a secondary pore zone. Overpressure broadened oil generation window, increased corrosion time and strength, making secondary pores developed in deeper formations. Moreover, the overpressure was beneficial to preserve pores. The reservoir economic basement depths of siltstone, very fine sandstone and fine sandstone are about 3 100 m, 3 900 m and 5 000 m respectively. The fine sandstone and very fine sandstone in the first member of the Huangliu Formation could form high-quality gas reservoirs in present depth of 2 600–3 500 m. Key words: submarine fan, thermal fluid, overpressure, economic basement, reservoir property, Yinggehai Basi

Overexpression of p62/IMP2 can Promote Cell Migration in Hepatocellular Carcinoma via Activation of the Wnt/β-Catenin Pathway

p62/IMP2 is an oncofetal protein that was first reported as a tumor-associated antigen in hepatocellular carcinoma (HCC). In our previous studies, we demonstrated a high frequency of p62/IMP2 autoantibodies appearing in various types of cancer. Therefore, we hypothesize that p62/IMP2 plays an important role in the progression of HCC, although the mechanism remains to be explored. In this study, we evaluated the expression of p62/IMP2 protein both in human tissues and liver cancer cell lines by immunohistochemistry and western blotting analysis and found that p62/IMP2 protein is overexpressed in human HCC tissue in comparison to normal human liver tissue. To explore the role that p62/IMP2 plays in HCC, p62/IMP2 was knocked out in two p62/IMP2-positive liver cancer cell lines (SNU449 and HepG2). Due to the low expression level of p62/IMP2 in SNU449, we overexpressed p62/IMP2 in this cell line. We subsequently demonstrated that high expression of p62/IMP2 in both cell lines can promote cell migration and invasion abilities in vitro by activating the Wnt/β-catenin pathway. We also used the Wnt/β-catenin pathway inhibitor, XAV 939, and a phosphoproteome assay to confirm our findings. Conclusion: Our results suggest that p62/IMP2 is an essential regulator of Wnt signaling pathways and plays an important role in HCC progression and metastasis