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Tuberculosis (TB) is a common infectious disease linked to host genetics and the innate immune response. It is vital to investigate new molecular mechanisms and efficient biomarkers for Tuberculosis because the pathophysiology of the disease is still unclear, and there aren’t any precise diagnostic tools. This study downloaded three blood datasets from the GEO database, two of which (GSE19435 and 83456) were used to build a weighted gene co-expression network for searching hub genes associated with macrophage M1 by the CIBERSORT and WGCNA algorithms. Furthermore, 994 differentially expressed genes (DEGs) were extracted from healthy and TB samples, four of which were associated with macrophage M1, naming RTP4, CXCL10, CD38, and IFI44. They were confirmed as upregulation in TB samples by external dataset validation (GSE34608) and quantitative real-time PCR analysis (qRT-PCR). CMap was used to predict potential therapeutic compounds for tuberculosis using 300 differentially expressed genes (150 downregulated and 150 upregulated genes), and six small molecules (RWJ-21757, phenamil, benzanthrone, TG-101348, metyrapone, and WT-161) with a higher confidence value were extracted. We used in-depth bioinformatics analysis to investigate significant macrophage M1-related genes and promising anti-Tuberculosis therapeutic compounds. However, more clinical trials were necessary to determine their effect on Tuberculosis.

Additional file 2: Supplementary materials and methods.

Additional file 1: Supplementary Figure 1 Normoxic AC16 cells were co-cultured with HR-EMVs at different concentrations (10^7, 10^8 and 10^9 particles/ml) for 24 h: (A) CCK-8 assay for AC16 cell viability. (B) Flow cytometry detection of apoptotic rate in AC16 cells after annexin V-FITC/PI double staining. (C) quantitative analysis of apoptotic cells. HR-injured AC16 cells were co-cultured with HR-EMVs, (HR + P25)-EMVs, (HR + P50)-EMVs, (HR + P100)-EMVs, and (HR + P150)-EMVs for 24 h, respectively: (D) CCK-8 assay for AC16 cell viability. (E) Flow cytometry detection of apoptotic rate in AC16 cells after annexin V-FITC/PI double staining. (F) quantitative analysis of apoptotic cells. These data were representative results (n = 3) of three repetitions. *P < 0.05, **P < 0.01, ***P < 0.001, ns, not significant. Data are expressed as mean ± SEM. Supplementary Figure 2 (A) HUVECs were infected with LV-sh-lncCCT4 or LV-sh-NC for 72 h. The knockdown efficiency of lncCCT4-2 in HUVECs was detected by RT-qPCR. Transfection of AC16 cells with sh-CCT4 and OE-CCT4 plasmids for 48 h: (B-C) Detection of CCT4 mRNA expression in AC16 cells by RT-qPCR. (D-E) Western blotting analysis of CCT4 protein expression in AC16 cells to detect the transfection efficiency of sh-CCT4 and OE-CCT4 plasmids. These data were representative results (n = 3) of three repetitions. *P < 0.05, **P < 0.01, ***P < 0.001, ns, not significant. Data are expressed as mean ± SEM. Supplementary 3 The genomic location and sequence of lncCCT4-2 and CCT4. Supplementary 4 Prediction of lncCCT4-2 and CCT4 mRNA binding sites.

The types, evolution processes, formation mechanisms, and depositional models of deep-water gravity flow deposits in a lacustrine rift basin are studied through core observation and systematic analysis. Massive transport of slide and slump, fluid transport of debris flow and turbidity currents are driven by gravity in deep-water lacustrine environment. The transformation between debris flow and turbidity current, and the transformation of turbidity current between supercritical and subcritical conditions are the main dynamic mechanisms of gravity flow deposits in a lake basin. The erosion of supercritical turbidity current controls the formation of gravity-flow channel. Debris flow deposition gives rise to tongue shape lobe rather than channel. Deep-water gravity flow deposits are of two origins, intrabasinal and extrabasinal. Intrabasinal gravity flow deposits occur as single tongue-shape lobe or fan of stacking multiple lobes. Extrabasinal gravity-flow deposits occur as sublacustrine fan with channel or single channel sand body. However, the nearshore subaqueous fan is characterized by fan of stacking multiple tongue shape lobes without channel. The differential diagenesis caused by differentiation in the nearshore subaqueous fan facies belt results in the formation of diagenetic trap. The extrabasinal gravity flow deposits are one of the important reasons for the abundant deep-water sand bodies in a lake basin. Slide mass-transport deposits form a very important type of lithologic trap near the delta front often ignored. The fine-grained sediment caused by flow transformation is the potential “sweet spot” of shale oil and gas.

Dolomitization is controlled by numerous interacting factors, causing the mechanism of dolomite reservoir formation to remain unclear. In particular, the influences of lithological minerals and crystal lattice characteristics on dolomitization may be the main driver of large-scale dolomite development. In this study, physical laboratory experiments involving the dissolution, precipitation, and transformation of carbonate minerals were conducted, along with real-time testing and analysis of rock samples and water samples, to determine the mechanism underlying metasomatic dolomitization. Additionally, multiple two-dimensional and three-dimensional homogeneous and heterogeneous numerical models were established. Changes in mineral content, ion concentration, and porosity were calculated using multiphase flow numerical simulation technology, and dolomitization was comparatively analyzed under various lithological conditions. The combination of physical experiments and numerical simulation effectively demonstrated the influence of dolomite crystal nucleus and lattice defects on dolomite formation. The presence of a dolomite crystal nucleus can promote the dissolution of calcite and allow more Mg to enter the calcite crystal lattice, promoting further dolomitization. Dolomitization occurs preferentially at lattice defects, and calcite grain boundaries break easily. The results of this study verify that surface conditions with low temperature and pressure are unsuitable for the development of dolomite, but microbes may produce small dolomite nuclei, leading to the large-scale development of dolomite. In the deep layer, because of defects in the crystal lattice, numerous pores form through dissolution. Because the lattice of deep dolomite is less stable than the lattice of limestone, dolomite has better physical properties than limestone after dissolution.

Lacustrine carbonate-rich shales are well developed within the Mesozoic-Cenozoic strata of the Bohai Bay Basin (BBB) of eastern China and across southeast Asia. Developing an understanding of the diagenesis of these shales is essential to research on mass balance, diagenetic fluid transport and exchange, and organic-inorganic interactions in black shales. This study investigates the origin and distribution of authigenic minerals and their diagenetic characteristics, processes, and pathways at the scale of lacustrine laminae within the Es4s-Es3x shale sequence of the BBB. The research presented in this study is based on thin sections, field emission scanning electron microscope (FESEM) and SEM-catholuminescence (CL) observations of well core samples combined with the use of X-ray diffraction (XRD), energy dispersive spectroscopy, electron microprobe analysis, and carbon and oxygen isotope analyses performed using a laser microprobe mass spectrometer. The dominant lithofacies within the Es4s-Es3x sequence are a laminated calcareous shale (LCS-1) and a laminated clay shale (LCS-2). The results of this study show that calcite recrystallization1 is the overarching diagenetic process affecting the LCS-1, related to acid generation from organic matter (OM) thermal evolution. This evolutionary transition is the key factor driving the diagenesis of this lithofacies, while the transformation of clay minerals is the main diagenetic attribute of the LCS-2. Diagenetic differences occur within different laminae and at variable locations within the same lamina level, controlled by variations in mineral composition and the properties of laminae interfaces. The diagenetic fluid migration scale is vertical and responses (dissolution and replacement) are limited to individual laminae, between zero and 100 μm in width. In contrast, the dominant migration pathway for diagenetic fluid is lateral, along the abrupt interfaces between laminae boundaries, which leads to the vertical transmission of diagenetic responses. The recrystallization boundaries between calcite laminae act as the main migration pathways for the expulsion of hydrocarbons from these carbonate-rich lacustrine shales. However, because the interaction between diagenetic fluids and the shales themselves is limited to the scale of individual lamina, this system is normally closed. The occurrence of abnormal pressure fractures can open the diagenetic system, however, and cause interactions to occur throughout laminae; in particular, the closed-open (C–O) diagenetic process at this scale is critical to this shale interval. Multi-scale C–O systems are ubiquitous and episodic ranging from the scale of laminae to the whole basin. Observations show that such small-scale systems are often superimposed onto larger ones to constitute the complex diagenetic system seen within the BBB combining fluid transport, material and energy exchange, and solid-liquid and organic-inorganic interactions.

According to porosity measured by high-pressure mercury intrusion experiments and helium, and analysis of oil saturation data of 30 samples of tight formations of Member 4 of Cretaceous Quantou Formation in Rangzijing slope zone, southern Songliao Basin, the lower limit of flowing porosity of tight oil and its controlling factors of the samples were determined. By conversion between capillary pressure in reservoir conditions and capillary pressure from high-pressure mercury intrusion experiments, flowing porosity in various injection pressures in reservoir condition can be calculated. By calculating the minimum flowing porosity of oil-bearing samples and the maximum flowing porosity of the samples without oil, it is confirmed that 3.2% is the lower limit of flowing porosity in the oil-bearing samples in the study area; and the corresponding injection pressure in reservoir conditions is 0.35 MPa. If the injection pressure is higher than 0.35 MPa, tight oil can effectively flow and accumulate. The flowing porosity of tight formations and pore-throat ratio are negatively related. When the connectivity of pore-throat in reservoirs becomes poorer, higher injection pressure is needed for flowing porosity to be 3.2%. The injection pressure needed for flowing porosity to be 3.2% have a negative correlation to reservoir quality coefficient. With the reservoir quality coefficient increasing, the injection pressure needed for flowing porosity to be 3.2% has a decreasing tendency. Based on the tight oil lower limit of flowing porosity and injection pressure in reservoir conditions, the discriminant chart of effective accumulation of tight oil was set up. Key words: southern Songliao Basin, Cretaceous, tight oil, lower limit of flowing porosity

Hydrocarbon distribution rules in the deep and shallow parts of sedimentary basins are considerably different, particularly in the following four aspects. First, the critical porosity for hydrocarbon migration is much lower in the deep parts of basins: at a depth of 7000 m, hydrocarbons can accumulate only in rocks with porosity less than 5%. However, in the shallow parts of basins (i.e., depths of around 1000 m), hydrocarbon can accumulate in rocks only when porosity is over 20%. Second, hydrocarbon reservoirs tend to exhibit negative pressures after hydrocarbon accumulation at depth, with a pressure coefficient less than 0.7. However, hydrocarbon reservoirs at shallow depths tend to exhibit high pressure after hydrocarbon accumulation. Third, deep reservoirs tend to exhibit characteristics of oil (–gas)–water inversion, indicating that the oil (gas) accumulated under the water. However, the oil (gas) tends to accumulate over water in shallow reservoirs. Fourth, continuous unconventional tight hydrocarbon reservoirs are distributed widely in deep reservoirs, where the buoyancy force is not the primary dynamic force and the caprock is not involved during the process of hydrocarbon accumulation. Conversely, the majority of hydrocarbons in shallow regions accumulate in traps with complex structures. The results of this study indicate that two dynamic boundary conditions are primarily responsible for the above phenomena: a lower limit to the buoyancy force and the lower limit of hydrocarbon accumulation overall, corresponding to about 10%–12% porosity and irreducible water saturation of 100%, respectively. These two dynamic boundary conditions were used to divide sedimentary basins into three different dynamic fields of hydrocarbon accumulation: the free fluid dynamic field, limit fluid dynamic field, and restrain fluid dynamic field. The free fluid dynamic field is located between the surface and the lower limit of the buoyancy force, such that hydrocarbons in this field migrate and accumulate under the influence of, for example, the buoyancy force, pressure, hydrodynamic force, and capillary force. The hydrocarbon reservoirs formed are characterized as “four high,” indicating that they accumulate in high structures, are sealed in high locations, migrate into areas of high porosity, and are stored in reservoirs at high pressure. The basic features of distribution and accumulation in this case include hydrocarbon migration as a result of the buoyancy force and formation of a reservoir by a caprock. The limit fluid dynamic field is located between the lower limit of the buoyancy force and the lower limit of hydrocarbon accumulation overall; the hydrocarbon migrates and accumulates as a result of, for example, the molecular expansion force and the capillary force. The hydrocarbon reservoirs formed are characterized as “four low,” indicating that hydrocarbons accumulate in low structures, migrate into areas of low porosity, and accumulate in reservoirs with low pressure, and that oil(–gas)–water inversion occurs at low locations. Continuous hydrocarbon accumulation over a large area is a basic feature of this field. The restrain fluid dynamic field is located under the bottom of hydrocarbon accumulation, such that the entire pore space is filled with water. Hydrocarbons migrate as a result of the molecular diffusion force only. This field lacks many of the basic conditions required for formation of hydrocarbon reservoirs: there is no effective porosity, movable fluid, or hydrocarbon accumulation, and potential for hydrocarbon exploration is low. Many conventional hydrocarbon resources have been discovered and exploited in the free fluid dynamic field of shallow reservoirs, where exploration potential was previously considered to be low. Continuous unconventional tight hydrocarbon resources have been discovered in the limit fluid dynamic field of deep reservoirs; the exploration potential of this setting is thought to be tremendous, indicating that future exploration should be focused primarily in this direction.

In order to investigate the microbes in formation water samples from Well Du 6-3 and Ao-7 in the Alaxin and Aonan gas fields, Songliao Basin, China, 16S rDNA was amplified by using the Polymerase Chain Reaction (PCR) technique with templates of the extracted DNA and primers of bacteria and archaea. The PCR products were also inserted into vectors and then ligated with competent cells for gene sequencing. Based on the obtained gene sequences, bacterial and archaeal libraries were constructed and microbiological phylogeny graphs were obtained for the samples to understand the structure of microbial community and deduce the possible pathways of methanogenesis. The result indicates that there are only a few types of microbes in the samples of the two wells. Pseudomonas and Methanobacterium are the dominant species in the microbial and archaeal libraries, respectively. It is concluded that the indigenous microbial community in Well Du 6-3 probably mainly generated methane by CO2 reduction, but methanogenesis of acetic acid could not be completely excluded. The methane from Well Ao-7 is shown to have been definitely converted from CO2. Therefore, methane generation via indigenous microbial metabolism may be ultimately realized by using the right method under favourable conditions in the two fields. Key words: biogas reservoir, polymerase chain reaction (PCR), methane bio-pathway, 16S rRNA clone library

Subtle traps or oil pools have become an important exploration play in the Dongying Depression, Bohai Bay Basin, east China. Despite recent successes in exploration, the formation mechanisms of subtle traps are still not well understood. The majority of subtle oil pools in the Dongying Depression are developed in the middle interval of the Es3 Member of the Paleogene Shahejie Formation with the subtle traps being primarily of lenticular basin-floor turbidite sands encompassed in mudstones. Oil in the subtle traps was previously thought to have migrated directly from the surrounding source rocks of the same formation (Es3). Detailed geochemical investigation of 41 oils and 41 rock samples from the depression now indicates that the oils from the subtle traps cannot be correlated well with the surrounding Es3 source rocks, which are characterized by high Pr/Ph (>1), low Gammacerane/C30hopane, representing a freshwater lacustrine setting. In contrast the oils features low Pr/Ph (

Based on the analysis of well logs, seismic data, core studies, the Dongying () Formation along the nearshore and adjacent sea areas, Bohai () Bay basin has been subdivided into three third-order sequences from base to top: namely, sequences SQ1, SQ2 and SQ3. The three sequences have different wireline (SP) log responses, showing triple-section characteristics with SQ1 being characterized by primarily flat baseline with intercalation of relatively low spontaneous potential, SQ2 generally exhibiting weak or moderate amplitude spontaneous potential with finger-shaped peaks, and SQ3 having relatively high spontaneous potential with funnel-shaped log curves. On the basis of the triple-section characteristics, the stratigraphic sequences can be correlated consistently throughout the entire study area. A stratigraphic and sedimentary model for sequences SQ1 to SQ3 of the Dongying Formation in the study area has been proposed. The accommodation space change in the two sides of the asymmetrical basin was examined and the asymmetrical basin has the feature of the asymmetrical accommodation space change. The asymmetrical physiography is a vital factor to influence the accommodation changes in additional to the lake level change, tectonism and sediment supply. This may have important implications to similar basins in other parts of China or elsewhere.

It is expected that crude oil production in China will maintain its current level until 2020. Driven by higher living standards and the rapid development of energy intensive industries, China's oil demand will increase rapidly and might lead to heavier import dependency. Three cases of demand forecasts are presented, but for the sake of sustainable economic and social development, neither the high nor the middle case is favourable for China. Thus, China must seek a path of oil saving economic development, and limit oil consumption to no more than 350MT in 2010 and 450MT in 2020. Meanwhile, in order to secure the oil supply, the following strategies should be adopted: save oil and develop alternative energies; stabilise domestic oil production and to diversify oil imports and overseas oil exploration and development; accelerate the gas industry and introduce strategic petroleum reserves.