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Abstract The occurrence of whole-genome duplication or polyploidy may promote plant adaptability to harsh environments. Here, we clarify the evolutionary relationship of eight GhCIPK6 homologous genes in upland cotton (Gossypium hirsutum). Gene expression and interaction analyses indicate that GhCIPK6 homologous genes show significant functional changes after polyploidy. Among these, GhCIPK6D1 and GhCIPK6D3 are significantly up-regulated by drought stress. Functional studies reveal that high GhCIPK6D1 expression promotes cotton drought sensitivity, while GhCIPK6D3 expression promotes drought tolerance, indicating clear functional differentiation. Genetic and biochemical analyses confirm the synergistic negative and positive regulation of cotton drought resistance through GhCBL1A1-GhCIPK6D1 and GhCBL2A1-GhCIPK6D3, respectively, to regulate stomatal movement by controlling the directional flow of K+ in guard cells. These results reveal differentiated roles of GhCIPK6 homologous genes in response to drought stress in upland cotton following polyploidy. The work provides a different perspective for exploring the functionalization and subfunctionalization of duplicated genes in response to polyploidization.

Abstract N6‐methyladenosine (m6A) is the most prevalent internal modification of mRNA and plays an important role in regulating plant growth. However, there is still a lack of effective tools to precisely modify m6A sites of individual transcripts in plants. Here, programmable m6A editing tools are developed by combining CRISPR/dCas13(Rx) with the methyltransferase GhMTA (Targeted RNA Methylation Editor, TME) or the demethyltransferase GhALKBH10 (Targeted RNA Demethylation Editor, TDE). These editors enable efficient deposition or removal of m6A modifications at targeted sites of endo‐transcripts GhECA1 and GhDi19 within a broad editing window ranging from 0 to 46 nt. TDE editor significantly decreases m6A levels by 24%–76%, while the TME editor increases m6A enrichment, ranging from 1.37‐ to 2.51‐fold. Furthermore, installation and removal of m6A modifications play opposing roles in regulating GhECA1 and GhDi19 mRNA transcripts, which may be attributed to the fact that their m6A sites are located in different regions of the genes. Most importantly, targeting the GhDi19 transcript with TME editor plants results in a significant increase in root length and enhanced drought resistance. Collectively, these m6A editors can be applied to study the function of specific m6A modifications and have the potential for future applications in crop improvement.

Abstract Global water scarcity and extreme weather intensify drought stress, significantly reducing cotton yield and quality worldwide. Drought treatments are conducted using a population of chromosome segment substitution lines generated from E22 (G. hirsutum) and 3–79 (G. barbadense) as parental lines either show superior yields or fiber quality under both control and drought conditions. Fourteen datasets, covering 4 yields and 4 quality traits, are compiled and assessed for drought resistance using the drought resistance coefficient (DRC) and membership function value of drought resistance (MFVD). Genome‐wide association studies, linkage analysis, and bulked segregant analysis are combined to analyze the DR‐related QTL. A total of 121 significant QTL are identified by DRC and MFVD of the 8 traits. CRISPR/Cas9 and virus‐induced gene silencing techniques verified DRR1 and DRT1 as pivotal genes in regulating drought resistant of cotton, with hap3‐79 exhibiting greater drought resistance than hapE22 concerning DRR1 and DRT1. Moreover, 14 markers with superior yield and fiber quality are selected for drought treatment. This study offers valuable insights into yield and fiber quality variations between G. hirsutum and G. barbadense amid drought, providing crucial theoretical and technological backing for developing cotton varieties resilient to drought, with high yield and superior fiber quality.

Abstract Background Cotton is a major world cash crop and an important source of natural fiber, oil, and protein. Drought stress is becoming a restrictive factor affecting cotton production. To facilitate the development of drought-tolerant cotton varieties, it is necessary to study the molecular mechanism of drought stress response by exploring key drought-resistant genes and related regulatory factors. Results In this study, two cotton varieties, ZY007 (drought-sensitive) and ZY168 (drought-tolerant), showing obvious phenotypic differences under drought stress, were selected. A total of 25,898 drought-induced genes were identified, exhibiting significant enrichment in pathways related to plant stress responses. Under drought induction, At subgenome expression bias was observed at the whole-genome level, which may be due to stronger inhibition of Dt subgenome expression. A gene co-expression module that was significantly associated with drought resistance was identified. About 90% of topologically associating domain (TAD) boundaries were stable, and 6613 TAD variation events were identified between the two varieties under drought. We identified 92 genes in ZY007 and 98 in ZY168 related to chromatin 3D structural variation and induced by drought stress. These genes are closely linked to the cotton response to drought stress through canonical hormone-responsive pathways, modulation of kinase and phosphatase activities, facilitation of calcium ion transport, and other related molecular mechanisms. Conclusions These results lay a foundation for elucidating the molecular mechanism of the cotton drought response and provide important regulatory locus and gene resources for the future molecular breeding of drought-resistant cotton varieties.

Abstract Background CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and crop genetic improvement. However, the editing efficiency of base editors at different targets varies greatly. Results Here, we develop a set of highly efficient base editors in cotton plants. GhABE8e, which is fused to conventional nCas9, exhibits 99.9% editing efficiency, compared to GhABE7.10 with 64.9%, and no off-target editing is detected. We further replace nCas9 with dCpf1, which recognizes TTTV PAM sequences, to broaden the range of the target site. To explore the functional divergence of TERMINAL FLOWER 1 (TFL1), we edit the non-coding and coding regions of GhTFL1 with 26 targets to generate a comprehensive allelic population including 300 independent lines in cotton. This allows hidden pleiotropic roles for GhTFL1 to be revealed and allows us to rapidly achieve directed domestication of cotton and create ideotype germplasm with moderate height, shortened fruiting branches, compact plant, and early-flowering. Further, by exploring the molecular mechanism of the GhTFL1 L86P and GhTFL1 K53G+S78G mutations, we find that the GhTFL1 L86P mutation weakens the binding strength of the GhTFL1 to other proteins but does not lead to a complete loss of GhTFL1 function. Conclusions This strategy provides an important technical platform and genetic information for the study and creation of ideal plant architecture.

Intracellular biothiols, including cysteine (Cys), glutathione (GSH), and homocysteine (Hcy), play a critical role in many physiological and pathological processes. Among them, GSH is the most abundant non-protein mercaptan (1–10 mM) in cells, and the change in GSH concentration level is closely related to the occurrence of many diseases, such as Parkinson’s disease, Alzheimer’s disease, and neurological diseases. Fluorescent probes have attracted much attention due to their advantages of high specificity, high sensitivity, high selectivity, low cost, and high quantum yield. Methods that use optical probes for selective detection of GSH in vitro and in vivo are in high demand. In this paper, we reviewed the most recent five years of research on fluorescence probes for the detection of GSH, including the specific detection of GSH, dual-channel identification of GSH and other substances, and the detection of GSH and other biothiols. According to the type of fluorophore, we classified GSH fluorescent probes into eight classes, including BODIPY, 1,8-Naphthalimide, coumarin, xanthene, rhodamine, cyanine, benzothiazoles, and others. In addition, we roundly discuss the synthesis, detection mechanism, photophysical properties, and biological applications of fluorescent probes. We hope that this review will inspire the exploration of new fluorescent probes for GSH and other related analyses.

Introduction: Drought is the principal abiotic stress that severely impacts cotton (Gossypium hirsutum) growth and productivity. Upon sensing drought, plants activate stress-related signal transduction pathways, including ABA signal and mitogen-activated protein kinase (MAPK) cascade. However, as the key components with the fewest members in the MAPK cascade, the function and regulation of GhMKKs need to be elucidated. In addition, the relationship between MAPK module and the ABA core signaling pathway remains incompletely understood. Objective: Here we aim to elucidate the molecular mechanism of cotton response to drought, with a focus on mitogen-activated protein kinase (MAPK) cascades activating ABA signaling. Methods: Biochemical, molecular and genetic analysis were used to study the GhMAP3K62-GhMKK16-GhMPK32-GhEDT1 pathway genes. Results: A nucleus- and membrane-localized MAPK cascade pathway GhMAP3K62-GhMKK16-GhMPK32, which targets and phosphorylates the nuclear-localized transcription factor GhEDT1, to activate downstream GhNCED3 to mediate ABA-induced stomatal closure and drought response was characterized in cotton. Overexpression of GhMKK16 promotes ABA accumulation, and enhances drought tolerance via regulating stomatal closure under drought stress. Conversely, RNAi-mediated knockdown of GhMKK16 expression inhibits ABA accumulation, and reduces drought tolerance. Virus-induced gene silencing (VIGS)-mediated knockdown of either GhMAP3K62, GhMPK32 or GhEDT1 expression represses ABA accumulation and reduces drought tolerance through inhibiting stomatal closure. Expression knockdown of GhMPK32 or GhEDT1 in GhMKK16-overexpressing cotton reinstates ABA content and stomatal opening-dependent drought sensitivity to wild type levels. GhEDT1 could bind to the HD boxes in the promoter of GhNCED3 to activate its expression, resulting in ABA accumulation. We propose that the MAPK cascade GhMAP3K62-GhMKK16-GhMPK32 pathway functions on drought response through ABA-dependent stomatal movement in cotton.

Abstract Background Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. Results We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. Conclusions This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.

In this letter, we propose an improved cosmological model independent method of determining the value of the Hubble constant H0. The method uses unanchored luminosity distances H0dL(z) from SN Ia Pantheon data combined with angular diameter distances dA(z) from a sample of intermediate luminosity radio quasars calibrated as standard rulers. The distance duality relation between dL(z) and dA(z), which is robust and independent of any cosmological model, allows to disentangle H0 from such combination. However, the number of redshift matched quasars and SN Ia pairs is small (37 data-points). Hence, we take an advantage from the Artificial Neural Network (ANN) method to recover the dA(z) relation from a network trained on full 120 radio quasar sample. In this case, the result is unambiguously consistent with values of H0 obtained from local probes by SH0ES and H0LiCOW collaborations. Three statistical summary measures: weighted mean H˜0=73.51(±0.67) km s−1 Mpc−1, median Med(H0)=74.71(±4.08) km s−1 Mpc−1 and MCMC simulated posterior distribution H0=73.52−0.68+0.66 km s−1 Mpc−1 are fully consistent with each other and the precision reached 1% level. This is encouraging for the future applications of our method. Because individual measurements of H0 are related to different redshifts spanning the range z=0.5−2.0, we take advantage of this fact to check if there is any noticeable trend in H0 measurements with redshift of objects used for this purpose. However, our result is that the data we used strongly support the lack of such systematic effects.

Dam construction has important impact on the ecological environment and navigation conditions of a river. Therefore, evaluating the degree of impact of such engineering constructions and seeking the optimum management are vital. This study considered the example of the construction of the Qingyuan Dam on the Beijiang River (China). The flow condition was calculated using a two-dimensional hydrodynamic model, and a habitat suitability model and navigation risk indicators were used to conduct quantitative assessment of the impact of different scenarios. The spawning ground habitat of Megalobrama terminalis was taken as an ecological measurement index. The gray correlation analysis method was used to quantify the influence of four flow indexes (i.e., water surface slope, backflow, flow velocity, and water depth) on navigation safety. The simulation results showed that construction of the Qingyuan Dam had serious negative impact on the ecological environment in the dry season, but that dry season navigation conditions have been improved greatly. Following construction of the dam, with increase in the Feilaixia Hydro-junction discharge, the ecological and navigable usable area both first increased and then decreased. With comprehensive consideration of the usable area and the spatial distributions of habitat suitability and navigation risk, when the Feilaixia Hydro-junction discharge is 3000 m3/s and the water level in front of the Qingyuan Dam is 10 m, the ecological and navigation benefits of the studied river reach were determined to be optimal. These research results could provide guidance for the management of the Feilaixia–Qingyuan river section, and help deliver optimum ecological and navigational benefits.

Gene expression has inherent stochasticity resulting from transcription's burst manners. Single-cell snapshot data can be exploited to rigorously infer transcriptional burst kinetics, using mathematical models as blueprints. The classical telegraph model (CTM) has been widely used to explain transcriptional bursting with Markovian assumptions. However, growing evidence suggests that the gene-state dwell times are generally non-exponential, as gene-state switching is a multi-step process in organisms. Therefore, interpretable non-Markovian mathematical models and efficient statistical inference methods are urgently required in investigating transcriptional burst kinetics. We develop an interpretable and tractable model, the generalized telegraph model (GTM), to characterize transcriptional bursting that allows arbitrary dwell-time distributions, rather than exponential distributions, to be incorporated into the ON and OFF switching process. Based on the GTM, we propose an inference method for transcriptional bursting kinetics using an approximate Bayesian computation framework. This method demonstrates an efficient and scalable estimation of burst frequency and burst size on synthetic data. Further, the application of inference to genome-wide data from mouse embryonic fibroblasts reveals that GTM would estimate lower burst frequency and higher burst size than those estimated by CTM. In conclusion, the GTM and the corresponding inference method are effective tools to infer dynamic transcriptional bursting from static single-cell snapshot data.

Reconstructing karst palaeogeomorphology is a useful approach to identifying target areas for oil and gas exploration. This study used the elevation method to reconstruct the karst palaeogeomorphology at the top of the 4th member (Z 2 dn 4 ) of the Dengying Formation (Z 2 dn) in the Central Sichuan Basin based on 2D and 3D seismic and drilling data. The bottom of the Longwangmiao Formation and the top of the 2nd member (Z 2 dn 2 ) of the Z 2 dn were optimized as the upper and lower base levels, respectively. The reconstructed palaeogeomorphology was divided into five types – slopes, erosional peneplains, monadnocks, domes and depressions – according to their morphology, scope and gradient, allowing inference of the palaeohydrological conditions. Slopes were subdivided into gentle (

Recently, industrial gas flows have been produced from the vertical well acidification tests of Wells JS1 and YH1 in Section 1 of the Maokou Formation in the southern region of eastern Sichuan Province, China. This result proves that Section 1 contains a group of excellent source rocks and gas-bearing reservoirs. In this study, the pore structure characteristics and primary causes of the nanopore structure were explored using scanning electron microscopy, X-ray diffraction of total rocks, total organic carbon, liquid nitrogen adsorption, and other experimental methods to determine the pore development features of nodular limestone reservoirs in Section 1. The results substantiate the presence of complex pore structures in the nodular limestone reservoirs in Section 1. Nanopores are dominant and mainly comprise micropores and mesopores approximately 4 nm in diameter. The pore forms are particularly schistose clay silt pores consisting of rigid particles and flask-shaped pores. N2 adsorption analysis showed that the specific surface area of the carbonate reservoir was 4.8842–8.1594 m2/g (mean = 6.0439 m2/g), and the pore volume was 0.008422–0.015098 cm3/g (mean = 0.043212 cm3/g). Mesopores were positively related to the total pore volume and total specific surface area, whereas macropore content had poorer correlations. Mesopores contribute more to the total pore volume and total specific surface area than macropores do. Spaces among the clay mineral layers (especially talcum gaps) predominantly contributed to the carbonate pore volume and specific surface area of the reservoir, and were positively related to the clay mineral content. The rocks have highly developed calcite pores, and their pore volumes and specific surface areas are negatively related to calcite pore content. Moreover, low organic content and low pore development degrees were observed. The organic content was weakly correlated with the pore volume and specific surface area, suggesting a low effect on reservoir performance. This assessment of the pore structure characteristics of Section 1 of the Maokou Formation yielded essential geological data that could inform the formulation of exploitation measures.

While transcription often occurs in a bursty manner, various possible regulations can lead to complex promoter patterns such as promoter cycles, giving rise to an important question: How do promoter kinetics shape transcriptional bursting kinetics? Here we introduce and analyze a general model of the promoter cycle consisting of multi-OFF states and multi-ON states, focusing on the effects of multi-ON mechanisms on transcriptional bursting kinetics. The derived analytical results indicate that burst size follows a mixed geometric distribution rather than a single geometric distribution assumed in previous studies, and ON and OFF times obey their own mixed exponential distributions. In addition, we find that the multi-ON mechanism can lead to bimodal burst-size distribution, antagonistic timing of ON and OFF, and diverse burst frequencies, each further contributing to cell-to-cell variability in the mRNA expression level. These results not only reveal essential features of transcriptional bursting kinetics patterns shaped by multi-state mechanisms but also can be used to the inferences of transcriptional bursting kinetics and promoter structure based on experimental data.

The lacustrine shale in the Da’anzhai member of Jurassic in the central Sichuan Basin is a key exploration target for shale oil and gas resources in China in the future. This paper presents a detailed study of shale rock types and component characteristics, shale pore types and structural characteristics, and shale pore evolution characteristics under thermal simulation conditions through experimental analyses such as rock thin section and field emission scanning electron microscopy (FE-SEM) observation, conventional physical property test, X-ray diffraction (XRD) analysis, TOC test, liquid nitrogen adsorption (LNA) test, and thermal simulation (pore) experiment. The results show that minerals in the Da’anzhai shale are mainly clay minerals, quartz, and calcite, with a small amount of feldspar, dolomite, and pyrite. In the shale oil reservoirs, there are dominantly inorganic pores (e.g. clay intergranular pores), and relatively few organic pores. The specific surface area ranges from 1.064 m 2 /g to 9.227 m 2 /g, with an average of 4.949 m 2 /g. The pore volume is 0.003–0.016 cm 3 /g, with an average of 0.010 cm 3 /g. Mesopores contribute the most to the total pore volume and total specific surface area. With the increase of thermal simulation temperature, the degree of shale thermal evolution increases, and the shale porosity increases, predominantly, owing to the contribution of organic pores. It is concluded that inorganic pores, especially clay intergranular pores, are the dominant pore type in the Da’anzhai shale oil reservoirs, and the evolution degree, burial time and depth of organic matter can obviously improve the organic pores.

Water conservancy projects may result in considerable economic and social benefits, though there is widespread concern about how their impact on aquatic ecosystems. However, there is no study about the combined effects of typical hydraulic structures (a dam and numerous spur dikes) on hydraulic habitat conditions. This is why the impacts of the construction of a dam and spur dikes in a reach of the Beijiang River between the Feilaixia and the Qingyuan on fish hydraulic habitat conditions are assessed. A habitat suitability model was established by coupling a two-dimensional (2-D) hydrodynamic model with habitat suitability curves. The coupled model then was used to simulate the spawning sites of Megalobrama terminalis (M. terminalis), calculate the usable habitat area (UHA), identify the spatial distribution of suitable spawning ground in the river reach, and analyze the habitat quality and hydraulic habitat diversity. The results show that the dam alone would negatively impact fish habitat, and cause the UHA to decrease by 35.5 % on average. The high-quality habitat area and the hydraulic habitat diversity decreased because of the dam. The spur dikes had positive effects and increased the UHA by 13.9 % on average. In addition, spur dikes increased the high-quality habitat area and enhanced the hydraulic habitat diversity. The lateral discontinuity resulting from spur dikes (the rate of UHA change, RC = 13.9 %) had less impact on the fish hydraulic habitat than the longitudinal discontinuity impact resulting from the dam construction (RC = − 35.5 %). The spur dikes and a dam (RC = 21.94 %) resulted in a more significant improvement effect on the habitat conditions than the spur dikes without a dam (RC = 5.84 %). The dam and spur dikes in combination resulted in better outcomes regarding hydraulic habitat conditions than spur dikes alone, and the spur dikes reduce the ecological stress caused by the dam. The insight from this study can serve as a reference for engineers and scientists who are considering similar river regulation and ecological restoration initiatives aimed at a steady flow pattern that are advantageous for a specific fish species and lifestage.

Based on outcrop characteristics, combined with regional tectonic background, drilling and geophysical data, the sedimentary characteristics of the Middle Permian Maokou Formation in the northern Sichuan Basin was studied by means of macroscopic and microscopic observation, geochemical element test, total organic carbon content and vitrinite reflectance measurement. There is a set of deep-water sediments rich in organic matter in the Guangyuan-Wangcang area of northern Sichuan during the late depositional period of the Middle Permian Maokou Formation. The strata are distributed from northwest to southeast, with thickness of 10–30 m, mainly composed of siliceous rocks and siliceous mudstones, intercalated with gravity flow deposits. Siliceous rocks and siliceous mudstones are characterized by thin single layer, flat bedding and rich siliceous radiolarians, calthrop and brachiopod with small body and thin shell, belonging to the typical sedimentary characteristics of deep-water trough facies. The contents of Cu, Co, Mo, Ni and the ratio of Ni to Co in the geochemical tests all indicate that the siliceous rocks are products of deep-water reducing environment. The TOC value ranges from 3.21% to 8.19%, with an average of 5.53%, indicating that the siliceous rocks have good hydrocarbon generation ability. The south side of the trough is in platform margin facies with high energy, and the sediments are mainly thick massive micritic-calcsparite biogenic (clastic) limestone, which is conducive to the formation and evolution of the reservoir. During the late sedimentary period of the Maokou Formation, the northward subduction and extension of the oceanic crust at the northwestern margin of the Yangtze Plate provided the internal dynamic conditions for the formation of the “Guangyuan-Wangcang” trough. According to the location, sedimentary characteristics and formation dynamics of the trough, it is similar to the “Kaijiang-Liangping” trough during Late Permian proposed by previous researchers. It is believed that the “Kaijiang-Liangping” trough already had its embryonic form during the Late Middle Permian.

The construction of water conservancy projects not only brings benefits such as flood control and disaster reduction but also has many effects on the habitat and reproduction of local aquatic organisms. Taking the reach from Xuzhuang Station to Gaocun Station in the lower Yellow River as an example, this paper discusses the effect of the Xiaolangdi Reservoir on the habitat of Yellow River carp (Cyprinus carpio). By constructing a two-dimensional hydrodynamic model, coupled with a habitat suitability model of the spawning ground of Yellow River carp, the weighted usable area (WUA) of the Yellow River carp habitat was calculated, and the spatial distribution of the habitat suitability index (HSI) in the reach was analyzed to evaluate habitat quality before and after the construction of the Xiaolangdi Reservoir. The results showed that the Xiaolangdi Reservoir had a negative effect on the habitat of Yellow River carp, resulting in the reduction of the spatial distribution of HSI, a decrease in WUA by 45.53%, and a decrease in habitat quality. The construction of the Xiaolangdi Reservoir reduced or even eliminated flow pulses in the downstream reach, but had little effect on the suitability index of water depth and velocity. However, the suitability index of water level rise was significantly reduced, which is not conducive to the spawning activities of aquatic organisms and has a negative effect on habitat. The results of this study will provide a reference for ecological restoration in this region.

As an important oil and gas-bearing area in the Tarim Basin, the Halahatang Area has great potential for resource exploration. However, the research on oil and gas sources and the filling period of the Lower Paleozoic Ordovician is still limited. In this study, the organic geochemical analysis of source rocks, the simulation technology of hydrocarbon generation evolution basin, the distribution characteristics of fluid inclusions, and the measurement of uniform temperature are used and combined with the stable isotope of natural gas and the characteristics of oil-source biomarkers, and the process of oil and gas accumulation is restored. The results show that: ①The Cambrian source rock is the main contributor to Ordovician crude oil in the Halahatang Area, and its crude oil shows the characteristics of lightweight, rich chain hydrocarbons, and poor aromatic hydrocarbons. The composition of C7 compound shows the advantage of n-heptane, which belongs to type I kerogen. The biomarker compounds show the characteristics of high content of long-chain tricyclic terpane and high Ts/Tm values, and the crude oil is considered to be a highly mature sapropelic kerogen source oil. ②The carbon isotopes of methane and ethane of Ordovician natural gas in the Halahatang Area are light (from −35.6 to −29.5‰), showing obvious characteristics of sapropelic gas. ③There are three stages of the oil and gas accumulation process in Ordovician reservoirs in the Halahatang Area. In the middle and late Caledonian periods, the source rock reached the hydrocarbon generation threshold and began to generate oil. The late Hercynian period was the main accumulation period, and the Himalayan period was dominated by dry gas filling. ④The crude oil generated in the Middle-Late Caledonian periods migrated along the faults and conductive layers and finally accumulated in the high parts of the structure in the north. The migration of oil and gas in the late Hercynian period was limited by the bitumen produced by early biodegradation. Since the asphalt plugging condensate gas has almost failed to cause gas invasion from the reservoir, the Ordovician reservoir still maintains the characteristics of crude oil-associated gas, forming an oil and gas reservoir with a gas cap.

The evaluation of reservoirs is of great importance in exploration practices, and reservoir distribution is dependent on multiple geological factors. The carbonate platform of the fourth member (Z2dn4) of the Dengying Formation (Z2dn) in the Gaoshiti-Moxi area (GMA) was uplifted above sea level during episode II of the Tongwan movement and underwent prolonged karstification by meteoric freshwater in the terminal Sinian, leading to a strong heterogeneity in reservoirs. Paleogeomorphology reflects hydraulic gradients that can affect the intensities of surface karstification and may be approximated by terrain slope gradients. Karst products (especially solution vugs and caverns) exist prevailingly in the Z2dn4; their development mirrors the extents of internal dissolution. Based on paleogeomorphological reconstruction using the elevation method, the slope angles of single boreholes were calculated through the digital elevation model (DEM). In accordance with single-borewell Fullbore Formation MicroImager (FMI) logging data, four electrofacies (host rock, vug, fracture, and cave) were identified in boreholes possessing FMI data. The identified electrofacies were matched with corresponding conventional logging curves to obtain the training data. A model generalized for other boreholes without FMI data was established with the random forest algorithm and the thicknesses of the four electrofacies in each borehole were determined to characterize the extent of karstification. Slope gradients and electrofacies thicknesses, together with multiple physical parameters of reservoirs in boreholes, were utilized for factor analysis. Four factors were obtained and fused into one comprehensive score based on their ratios of variance proportions. The favorability of reservoirs was described by the comprehensive scores of each borehole. These analyses showed that the most advantageous reservoirs are distributed in the vicinity of the platform margin in the west of the GMA, where they enjoy several benefits. Deposition of porous mound-shoal complexes occurs predominantly in the platform margin where large-scale caves are more developed in the mixing karst zone of seawater and freshwater. Meanwhile, the transmeridional lateral migration of hydrocarbons from the regional hydrocarbon-generating center abutting the west of the GMA contributes to earlier entrapment and accumulation in the mound-shoal complexes in the platform margin.

As the main byproduct of cotton fiber, the cotton seed yields about 1.6 times that of fiber, with its oil rich in unsaturated fatty acids, mainly linoleic acid. It is desirable for breeders to increase the oil content of cottonseed without affecting the yield and quality of cotton fiber. In this study, a seed-specific promoter- (alpha-globulin gene promoter-) driven GhDGAT1 overexpression vector (PαGlob-GhDGAT1) was constructed and used to transform an upland cotton line YZ1 (Gossypium hirsutum). Overexpression of the cotton gene GhDGAT1 in cotton seeds increased its total oil content from 4.7% to 13.9% in different transgenic lines and different generations. With the increase of oil content, the composition and contents of the main fatty acids in cotton seed also changed, as reflected by the contents of the main saturated fatty acids and unsaturated oleic acid. GhDGAT1 could be used to increase oil content and improve oil composition in cottonseed.

Abstract Background Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis. Results Through transcriptome analysis in cotton leaves under salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8 436, 11 628 and 6 311 differentially expressed genes (DEGs) in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signaling pathways, such as abscisic acid (ABA) and jasmonic acid (JA) signaling, calcium signaling, mitogen-activated protein kinase (MAPK) signaling cascade, transcription factors, activation of antioxidant and ion transporters, were participated in regulating salt response in cotton. Conclusions Our research not only contributed to understand the mechanism of cotton response to salt stress, but also identified nine candidate genes, which might be useful for molecular breeding to improve salt-tolerance in cotton.

Global warming is limiting availability of water resources in arid and semi-arid regions, and so understanding water use efficiency (WUE) is increasingly important for agricultural production in those areas. As China is the largest cotton producing area, the problem of balancing WUE and efficient cotton production is a major issue. In this study, we used a natural population of 517 Upland cotton accessions to conduct a water-controlled trial in south and north of Xinjiang over two years. A total of 18 traits including agronomic traits, fiber yield indices and fiber quality indices, were investigated for broad-sense heritability and coefficient of variation. Appropriate water limitation was found to promote the establishment of favorable agronomic traits in cotton, associated with an increased cotton yield of 8.46% in Xinjiang, at the expense of a certain degree of fiber quality, such as decreased fiber length and an over-higher micronaire value. We detected 33 QTL related to response to water limitation using a drought resistance coefficient (DRC), and 6 QTL were found using a comprehensive indicator of CIDT (comprehensive index of drought tolerance) at the genetic level by integrating resequencing data. Two novel QTL-hotspots including six differentially expressed genes (DEGs) were further identified related to the drought response of cotton. These findings not only suggested a new approach to irrigation of cotton fields in Xinjiang, but also provided abundant genetic evidence for genetic breeders to study drought improvement of crops.

HuR (human antigen R), an mRNA-binding protein responsible for poor prognosis in nearly all kinds of malignancies, is a potential anti-tumor target for drug development. While screening HuR inhibitors with a fluorescence polarization (FP) based high-throughput screening (HTS) system, the clinically used drug eltrombopag was identified. Activity of eltrombopag on molecular level was verified with FP, electrophoretic mobility shift assay (EMSA), simulation docking and surface plasmon resonance (SPR). Further, we showed that eltrombopag inhibited in vitro cell proliferation of multiple cancer cell lines and macrophages, and the in vivo anti-tumor activity was also demonstrated in a 4T1 tumor-bearing mouse model. The in vivo data showed that eltrombopag was efficient in reducing microvessels in tumor tissues. We then confirmed the HuR-dependent anti-angiogenesis effect of eltrombopag in 4T1 cells and RAW264.7 macrophages with qRT-PCR, HuR-overexpression and HuR-silencing assays, RNA stability assays, RNA immunoprecipitation and luciferase assays. Finally, we analyzed the in vitro anti-angiogenesis effect of eltrombopag on human umbilical vein endothelial cells (HUVECs) mediated by macrophages with cell scratch assay and in vitro Matrigel angiogenesis assay. With these data, we revealed the HuR-dependent anti-angiogenesis effect of eltrombopag in breast tumor, suggesting that the existing drug eltrombopag may be used as an anti-cancer drug.

The basic leucine zipper (bZIP) transcription factors, which harbor a conserved bZIP domain composed of two regions, a DNA-binding basic region and a Leu Zipper region, operate as important switches of transcription networks in eukaryotes. However, this gene family has not been systematically characterized in cotton (Gossypium hirsutum). Here, we identified 197 bZIP family members in cotton. The chromosome distribution pattern indicates that the GhbZIP genes have undergone 53 genome-wide segmental and 7 tandem duplication events which contribute to the expansion of the cotton bZIP family. Phylogenetic analysis showed that cotton GhbZIP proteins cluster into 13 subfamilies, and homologous protein pairs showed similar characteristics. Inspection of the DNA-binding basic region and leucine repeat heptads within the bZIP domains indicated different DNA-binding site specificities as well as dimerization properties among different groups. Comprehensive expression analysis indicated the most highly and differentially expressed genes in root and leaf that might play significant roles in cotton response to drought stress. GhABF3D was identified as a highly and differentially expressed bZIP family gene in cotton leaf and root under drought stress treatments that likely controls drought stress responses in cotton. These data provide useful information for further functional analysis of the GhbZIP gene family and its potential application in crop improvement.

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate (RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt (the relative germination rates of seeds under salt stress), RGR-Cold (the relative germination rates of seeds under cold stress), and DIV (the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP (best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs (i02237Gh, i02243Gh) on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval (D01, 37771–1942912). Of these four genes, GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton. Keywords: Upland cotton, Stress, Relative germination rate, SSR, SNP, Candidate gene

Abstract Background Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton. Results Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in Gossypium arboreum, 149 in G. raimondii, 267 in G. barbadense and 283 in G. hirsutum. Predicted membrane-bound NAC genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of NAC genes occurred between diploid and polyploid cotton species, and variation analysis showed GhNAC genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes. Comprehensive expression analysis indicated that 38 GhNAC genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated NAC genes and secondary cell wall (SCW) biosynthesis genes. Conclusions NAC genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.

Aims: There may exist an effect modification of hypertension on the relation of vitamin D deficiency with cardiovascular disease. The aim of this study was to investigate this interaction on coronary heart disease. Methods: We investigated 348 consecutive patients (mean age 62.4 ± 10.5 years; 56.3% male) who underwent coronary angiography because of chest discomfort at our heart center. Serum 25-OH vitamin D was also detected by ELISA method in these patients. Multivariable logistic regression models were used to estimate odd ratios (ORs) of CHD across vitamin D levels in hypertensives and normotensives, respectively. Results: We found the multivariable-adjusted ORs of CHD in the bottom(≤8.5 ng/ml) and middle tertiles (8.5–13 ng/ml) of 25-OH vitamin D were 2.86 (95% confidence interval [CI]: 1.38, 5.92) and 1.63 (0.83, 3.20), respectively, compared with those in top tertiles (>13ng/ml) among hypertensives (Ptrend=0.005). In contrast, the corresponding ORs of the above two groups were 0.88 (0.28, 2.74) and 1.23 (0.42, 4.00), respectively, in the normotensives (Ptrend = 0.800; Peffect modification = 0.020). The multivariable-adjusted OR of CHD in patients with severe hypovitaminosis D (

Cotton, a natural fiber producing crop of huge importance, is often prone to attack of Verticillium dahliae. Papain-like cysteine proteases (PLCPs) constitute a large family in plants and were proposed to involve in plant defense against pathogen attack in a number of studies. However, there is no detailed characterization of PLCP genes in cotton against infection of V. dahliae. In this study, we carried out a genome-wide analysis in cotton and identified seventy-eight PLCPs, which were divided into nine subfamilies based on their evolution phylogeny: RD21 (responsive to desiccation 21), CEP (cysteine endopeptidase), XCP (xylem cysteine peptidase), XBCP3 (xylem bark cysteine peptidase 3), THI, SAG12 (senescence-associated gene 12), RD19 (responsive to desiccation 19), ALP (aleurain-like protease) and CTB (cathepsin B-like). Genes in each subfamily exhibit a similar structure and motif composition. The expression patterns of these genes in different organs were examined, and subfamily RD21 was the most abundant in these families. Expression profiles under abiotic stress showed that thirty-five PLCP genes were induced by multiple stresses. Further transcriptome analysis showed that sixteen PLCP genes were up-regulated in response to V. dahliae in cotton. Among those, GhRD21-7 showed a higher transcription level than most other PLCP genes. Additionally, over-expression of GhRD21-7 led to enhanced resistance and RNAi lines were more susceptible to V. dahliae in cotton. Our results provide valuable information for future functional genomic studies of PLCP gene family in cotton.

The ecological environment is the foundation of human survival and development, and forest ecosystem nature reserves play an important role in the protection of the ecological environment. The evaluation of forest ecosystem nature reserves facilitates the formulation of relevant management policies. At present, the evaluation of the ecological environment of forest ecosystem nature reserves is mainly based on detailed evaluation of some elements of the ecological environment, rather than on a comprehensive quantitative evaluation that reflects the ecological environment in many aspects. To address this shortcoming, the quantitative evaluation indicator system of comprehensive ecological environment for forest ecosystem nature reserves was established based on the water, air, soil, and biological environments, according to the consensus on ecological environment in the past research and characteristics of the research area. The weight is still a necessary and important link in the evaluation of forest ecosystem nature reserves, but the accuracy of the weight results is difficult to get a scientific judgment. To prevent the evaluation results being influenced by weighting uncertainty, an unweighted cloud model was constructed to provide an evaluation mechanism without weight. The ecological environment evaluation was then carried out using the unweighted cloud model, taking Songshan Nature Reserve as a research area. The results show that the grades of the ecological environment of Songshan Nature Reserve are 21% excellent, 67% good, and 12% qualified, and that the state of the ecological environment is stable and performing well. The evaluation results for the grades of the environmental dimension layers are water environment > soil environment > biological environment > air environment. The study’s research results can provide theoretical support for the evaluation of forest ecosystem nature reserves, and for evaluation work in general when weights are difficult to determine or uncertain.

The engineering applications of two-dimensional (2D) hydrodynamic models are restricted by the enormous number of meshes needed and the overheads of simulation time. The aim of this study is to improve computational efficiency and optimize the balance between the quantity of grids used in and the simulation accuracy of 2D hydrodynamic models. Local mesh refinement and a local time stepping (LTS) strategy were used to address this aim. The implementation of the LTS algorithm on a 2D shallow-water dynamic model was investigated using the finite volume method on unstructured meshes. The model performance was evaluated using three canonical test cases, which discussed the influential factors and the adaptive conditions of the algorithm. The results of the numerical tests show that the LTS method improved the computational efficiency and fulfilled mass conservation and solution accuracy constraints. Speedup ratios of between 1.3 and 2.1 were obtained. The LTS scheme was used for navigable flow simulation of the river reach between the Three Gorges and Gezhouba Dams. This showed that the LTS scheme is effective for real complex applications and long simulations and can meet the required accuracy. An analysis of the influence of the mesh refinement on the speedup was conducted. Coarse and refined mesh proportions and mesh scales observably affected the acceleration effect of the LTS algorithm. Smaller proportions of refined mesh resulted in higher speedup ratios. Acceleration was the most obvious when mesh scale differences were large. These results provide technical guidelines for reducing computational time for 2D hydrodynamic models on non-uniform unstructured grids.

The origin of the organic-rich shale in the Upper Ordovician Wufeng Formation and Lower Silurian Longmaxi Formation is complex and controversial. This paper reports the geochemical data of Wufeng-Longmaxi Formations in the Upper Yangtze region to restore the paleoenvironment and explore the accumulation mechanism of organic matter. The total organic carbon (TOC) content of the Wufeng Formation was relatively high, with an average of 2.86%. The Lower Longmaxi Formation showed the highest TOC content, with an average of 3.99%, and the upper part was a continuously low value with an average of 1.22%. The paleoproductivity proxies (Babio, Cu/Al, Ni/Al, Siexcess) showed that in the Katian and Rhuddanian-Aeronian Stages, the Upper Yangtze Sea had high primary productivity, indicating that organic matter accumulation was more affected by terrigenous influx and redox conditions. Al, Zr, and Zr/Al indicated that terrigenous influx was relatively high in the Kaitian-Hirnantian Stages, it was at a constant low in the Rhuddanian Stage, and increased again in the Aeronian Stage. The correlations between redox-sensitive trace elements (Mo, U, V) and TOC indicate that the organic-rich shale of the Wufeng Formation was deposited in the anoxic−euxinic environment. In the Longmaxi Formation, organic-rich shales formed in a more hypoxic environment, and overlying organic-lean shales formed in a suboxic environment. Therefore, the anoxic−euxinic conditions of the Late Ordovician Yangtze Sea were the main reason for the organic matter accumulation, but the high terrigenous influx caused by regression and/or structural controls diluted the organic matter to some extent. For the Early Silurian, a complete transgression−regression cycle changed terrigenous influx and redox conditions, resulting in significant differences in organic matter accumulation.

DNA methylation is an essential epigenetic modification involved in regulating the expression of mammalian genomes. A variety of experimental approaches to generate genome-wide or whole-genome DNA methylation data have emerged in recent years. Methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) is one of the major tools used in whole-genome epigenetic studies. However, analyzing this data in terms of accuracy, sensitivity, and speed still remains an important challenge. Existing methods, such as BATMAN and MEDIPS, analyze MeDIP-seq data by dividing the whole genome into equal length windows and assume that each CpG of the same window has the same methylation level. More precise work is necessary to estimate the methylation level of each CpG site in the whole genome. In this paper, we propose a Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site. In addition, we analyze a real dataset for DNA methylation. The results show that our method displays improved precision in detecting differentially methylated CpG sites compared to the existing method. To meet the demands of the application, we have developed an R package called "SIMD", which is freely available in https://github.com/FocusPaka/SIMD.

To achieve secure communication in heterogeneous cryptography systems, we present a heterogeneous hybrid signcryption scheme. The proposed scheme allows a sender in an identity-based cryptography system to send multi-message to multi-receiver in a certificateless cryptography system with different master keys. At the same time, all users are mapped to a distinct pseudo-identity for conditional identity privacy preservation. A trusted authority could trace the real identity when necessary. Compared with existing schemes, the proposed scheme is more practical for actual applications. In addition, the proposed scheme has indistinguishability against adaptive chosen ciphertext attacks and existential unforgeability against adaptive chosen message attacks under the random oracle model.

BACKGROUND:Plants often face multiple stresses including drought, extreme temperature, salinity, nutrition deficiency and biotic stresses during growth and development. All the stresses result in a series of physiological and metabolic reactions and then generate reversible inhibition of metabolism and growth and can cause seriously irreversible damage, even death. At each stage of cotton growth, environmental stress conditions pose devastating threats to plant growth and development, especially yield and quality. Due to the complex stress conditions and unclear molecular mechanisms of stress response, there is an urgent need to explore the mechanisms of cotton response against abiotic stresses. METHODOLOGY AND PRINCIPAL FINDINGS:A normalized cDNA library was constructed using Gossypium barbadense Hai-7124 treated with different stress conditions (heat, cold, salt, drought, potassium and phosphorus deficit and Verticillium dahliae infection). Random sequencing of this library generated 6,047 high-quality expressed sequence tags (ESTs). The ESTs were clustered and assembled into 3,135 uniESTs, composed of 2,497 contigs and 638 singletons. The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized. Functional classification unveiled the abundance of uniESTs in binding, catalytic activity, and structural molecule activity. Annotations of the uniESTs by the plant transcription factor database (PlantTFDB) and Plant Stress Protein Database (PSPDB) disclosed that transcription factors and stress-related genes were enriched in the current library. The expression of some transcription factors and specific stress-related genes were verified by RT-PCR under various stress conditions. CONCLUSIONS/SIGNIFICANCE:Annotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF. These results will improve our knowledge of stress tolerance in cotton. In addition, they are also helpful in discovering candidate genes related to stress tolerance. The publicly available ESTs from G. barbadense are a valuable genomic resource that will facilitate further molecular study and breeding of stress-tolerant cotton.

As a second messenger, Ca(2+) plays a major role in cold induced transduction via stimulus-specific increases in [Ca(2+)]cyt, which is called calcium signature. During this process, CAXs (Ca(2+)/H(+) exchangers) play critical role. For the first time, a putative Ca(2+)/H(+) exchanger GhCAX3 gene from upland cotton (Gossypium hirsutum cv. 'YZ-1') was isolated and characterized. It was highly expressed in all tissues of cotton except roots and fibers. This gene may act as a regulator in cotton's response to abiotic stresses as it could be up-regulated by Ca(2+), NaCl, ABA and cold stress. Similar to other CAXs, it was proved that GhCAX3 also had Ca(2+) transport activity and the N-terminal regulatory region (NRR) through yeast complementation assay. Over-expression of GhCAX3 in tobacco showed less sensitivity to ABA during seed germination and seedling stages, and the phenotypic difference between wild type (WT) and transgenic plants was more significant when the NRR was truncated. Furthermore, GhCAX3 conferred cold tolerance in yeast as well as in tobacco seedlings based on physiological and molecular studies. However, transgenic plant seeds showed more sensitivity to cold stress compared to WT during seed germination, especially when expressed in N-terminal truncated version. Finally, the extent of sensitivity in transgenic lines was more severe than that in WT line under sodium tungstate treatment (an ABA repressor), indicating that ABA could alleviate cold sensitivity of GhCAX3 seeds, especially in short of its NRR. Meanwhile, we also found that overexpression of GhCAX3 could enhance some cold and ABA responsive marker genes. Taken together, these results suggested that GhCAX3 plays important roles in the cross-talk of ABA and cold signal transduction, and compared to full-length of GhCAX3, the absence of NRR could enhance the tolerance or sensitivity to cold stress, depending on seedling's developmental stages.