Forecast of lacustrine shale lithofacies types in continental rift basins based on machine learning: A case study from Dongying Sag, Jiyang Depression, Bohai Bay Basin, China

Lacustrine shale in continental rift basins is complex and features a variety of mineralogical compositions and microstructures. The lithofacies type of shale, mainly determined by mineralogical composition and microstructure, is the most critical factor controlling the quality of shale oil reservoirs. Conventional geophysical methods cannot accurately forecast lacustrine shale lithofacies types, thus restricting the progress of shale oil exploration and development. Considering the lacustrine shale in the upper Es4 member of the Dongying Sag in the Jiyang Depression, Bohai Bay Basin, China, as the research object, the lithofacies type was forecast based on two machine learning methods: support vector machine (SVM) and extreme gradient boosting (XGBoost). To improve the forecast accuracy, we applied the following approaches: first, using core and thin section analyses of consecutively cored wells, the lithofacies were finely reclassified into 22 types according to mineralogical composition and microstructure, and the vertical change of lithofacies types was obtained. Second, in addition to commonly used well logging data, paleoenvironment parameter data (Rb/Sr ratio, paleoclimate parameter; Sr %, paleosalinity parameter; Ti %, paleoprovenance parameter; Fe/Mn ratio, paleo-water depth parameter; P/Ti ratio, paleoproductivity parameter) were applied to the forecast. Third, two sample extraction modes, namely, curve shape-to-points and point-to-point, were used in the machine learning process. Finally, the lithofacies type forecast was carried out under six different conditions. In the condition of selecting the curved shape-to-point sample extraction mode and inputting both well logging and paleoenvironment parameter data, the SVM method achieved the highest average forecast accuracy for all lithofacies types, reaching 68%, as well as the highest average forecast accuracy for favorable lithofacies types at 98%. The forecast accuracy for all lithofacies types improved by 7%–28% by using both well logging and paleoenvironment parameter data rather than using one or the other, and was 7%–8% higher by using the curve shape-to-point sample extraction mode compared to the point-to-point sample extraction mode. In addition, the learning sample quantity and data value overlap of different lithofacies types affected the forecast accuracy. The results of our study confirm that machine learning is an effective solution to forecast lacustrine shale lithofacies. When adopting machine learning methods, increasing the learning sample quantity (>45 groups), selecting the curve shape-to-point sample extraction mode, and using both well logging and paleoenvironment parameter data are effective ways to improve the forecast accuracy of lacustrine shale lithofacies types. The method and results of this study provide guidance to accurately forecast the lacustrine shale lithofacies types in new shale oil wells and will promote the harvest of lacustrine shale oil globally

Complement Activity in the Egg Cytosol of Zebrafish Danio rerio: Evidence for the Defense Role of Maternal Complement Components

Most fish embryos that develop externally are exposed to an environment full of microbes. How they survive microbial attacks are not understood to date. Here we demonstrated that the egg cytosol prepared from the newly fertilized eggs of zebrafish Danio rerio is capable of killing the Gram-negative bacterium Escherichia coli, via in vitro assay system of the complement activity established. All findings indicate that it is the complement system operating via the alternative pathway that is attributable to the bacteriolytic activity. This is the first report providing the evidence for the functional role of the maternal complement components in fish eggs, paving the way for study of maternal immunity in other organisms whose eggs are fertilized in vitro

Influences of antibodies and chemical inhibitors on the bateriolytic activity of zebrafish egg cytosol.

<p>The egg cytosol was pre-incubated with complement component antibodies and chemicals at optimum concentrations, and mixed with <i>E. coli</i> suspension. After incubation at 25°C for 2 h, the bacteriolytic activities were measured by colony forming unit assay.</p

Effects of divalent cation chelators EGTA and EGTA on the bacteriolytic activity of zebrafish egg cytosol.

<p>The egg cytosol was pre-incubated with EGTA, EDTA, EDTA with Mg²⁺ or EDTA with Ca²⁺ at optimum concentrations, and then mixed with <i>E. coli</i> suspension. After incubation at 25°C for 2 h, the bacteriolytic activities were measured by colony forming unit assay.</p

Characteristics of bacteriolytic activity in zebrafish egg cytosol.

<p>The egg cytosol filtered through 0.22 µm filter was mixed with <i>E. coli</i> suspension and incubated at 25°C for different periods (A) or at different temperature for 2 h (B). The bacteriolytic activities were determined by colony forming unit assay.</p

Effects of anti-C3 antibody and heating on the bacteriolytic activity of zebrafish egg cytosol.

<p>The egg cytosol was pre-incubated with anti-C3 antibody at different concentrations (A), or inactivated by heating at 45°C (B), and then mixed with <i>E. coli</i> suspension. After incubation at 25°C for 2 h, the bacteriolytic activities were measured by colony forming unit assay. * means <i>p</i><0.05.</p

Western blot analysis of C3 and Bf in zebrafish egg cytosol (lane M: molecular marker; lane H: human serum; lane Z: zebrafish egg cytosol).

<p>The egg cytosol was electrophoresed on 12% SDS-PAGE gel using the buffer system of Laemmli. The proteins separated were blotted on nitrocellulose membrane and immunostained with rabbit anti-human C3 antibody or goat anti-human Bf antibody, followed by staining with HRP-labeled anti-rabbit IgG and HRP-labeled anti-goat IgG, respectively.</p

Aquareovirus NS80 Initiates Efficient Viral Replication by Retaining Core Proteins within Replication-Associated Viral Inclusion Bodies

<div><p>Viral inclusion bodies (VIBs) are specific intracellular compartments for reoviruses replication and assembly. Aquareovirus nonstructural protein NS80 has been identified to be the major constituent for forming globular VIBs in our previous study. In this study, we investigated the role of NS80 in viral structural proteins expression and viral replication. Immunofluorescence assays showed that NS80 could retain five core proteins or inner-capsid proteins (VP1-VP4 and VP6), but not outer-capsid proteins (VP5 and VP7), within VIBs in co-transfected or infected cells. Further co-immunoprecipitation analysis confirmed that NS80 could interact with each core protein respectively. In addition, we found that newly synthesized viral RNAs co-localized with VIBs. Furthermore, time-course analysis of viral structural proteins expression showed that the expression of NS80 was detected first, followed by the detection of inner shell protein VP3, and then of other inner-capsid proteins, suggesting that VIBs were essential for the formation of viral core frame or progeny virion. Moreover, knockdown of NS80 by shRNA not only inhibited the expression of aquareovirus structural proteins, but also inhibited viral infection. These results indicated that NS80-based VIBs were formed at earlier stage of infection, and NS80 was able to coordinate the expression of viral structural proteins and viral replication.</p></div

Knockdown of NS80 impaired virus replication.

<p>(A) HEK 293T cells were co-transfected with each shRNA construct and pCI-neo-NS80. All the treated cells were analyzed by WB at 24 h post-transfection. (B) CIK cells transfected without (mock) or with each shRNA construct were infected with GCRV at MOI of 1 at 24 h post-transfection. Cell supernatants were collected at 24 h post-infection and virus titers were tested by TCID50 assay. (C) CIK cells transfected with shRNA-control (shRNA-ctr) or shRNA-2(shRNA-2) were mock infected (-) or infected with GCRV (+) at MOI of 1 at 24 h post-transfection and then analyzed by WB or RT-PCR at 24 h post-infection. (D) Relative mRNA change level in NS80 knockdown cells. All relative mRNA level in shRNA-2 transefcted cells was balanced to β-actin and evaluated to samples of shRNA-control transfected cells. The data represent means plus standard deviations for three independent experiments. Statistical analysis was performed using Student’s <i>t</i> test. ** indicates <i>P</i><0.01.</p