Enrichment Patterns Research Articles

Research on the Biogas Production Mechanism of Mudstone in the Qaidam Basin under Different CO2 Pressures.

Mudstone, a class of sedimentary rocks rich in organic matter, possesses considerable potential for biogas production. Mudstones possess a rich biological origin, which is conducive to refining the mechanisms and enrichment patterns of biogenic gas reservoirs. This has significant theoretical and practical implications for guiding the exploration and development of Quaternary mudstone gas reservoirs. Furthermore, the Qaidam Basin is an excellent place for the geological storage of CO2 due to its rich petroleum reservoir conditions. Experimental research on biogas production under diverse CO2 pressure-mudstone-microorganism-water interactions is conducted to determine the biogas production mechanism of mudstone under different CO2 pressures during sequestration circumstances. According to the results: (1) under supercritical carbon dioxide conditions, there is a slight initial increase in biogas production, followed by a gradual decrease. The periods and peaks of gas production vary among the different reaction groups. As carbon dioxide pressure increases, the gas production cycle lengthens significantly, while the gas yield declines. (2) Siderite and secondary carbonate minerals have increased in the mudstone's mineral fraction both before and after biogas production, while clay mineral groups have decreased. Specifically, there was a notable drop in chlorite and kaolinite. (3) Microorganism species in the system were analyzed, and the results showed that there was a gap in each microorganism's ability to adapt to its surroundings, and the diversity and quantity of bacteria declined with increasing pressure. After carbon dioxide was fluxed, there was a considerable shift in the pattern of biogas generation, which consequently had a major impact on the alterations in mineral fractions.

Chemical classification of spherules recovered from the Pacific Ocean site of the CNEOS 2014-01-08 (IM1) bolide

We have conducted an extensive towed-magnetic-sled survey during the period of June 14–28, 2023, over the seafloor about 85 km north of Manus Island, Papua New Guinea, centered around the calculated path of the bolide CNEOS 2014-01-08 (IM1). We found about 850 spherules of diameter 0.1–1.3 mm in our samples. The samples were analyzed by micro-XRF, Electron Probe Microanalyzer and ICP Mass spectrometry. Here we report major and trace element compositions of the samples and classify spherules based on that analysis. We identified 78 % of the spherules as primitive, in that their compositions have not been affected by planetary differentiation. We divided these into four groups, three of which correspond to previously described cosmic spherule types. Spherules in the fourth group, comprising 22 % of the collection, appear to all reflect planetary igneous differentiation and are all different from previously described spherules. We call them D-type spherules. At least five of the D-type spherules are suggested to be terrestrial in origin, although many spherules exhibit elemental ratios that are distinct from known planetary bodies and their origins are undetermined. A subset of the D-spherules show an excess of Be, La and U, by up to three orders of magnitude relative to the solar system standard of CI chondrites. Detailed mass spectrometry of 12 of these “BeLaU”-type spherules, the population of which may constitute up to ∼10 % of our entire collected sample, suggests that they are derived from material formed by planetary igneous fractionation. Their chemical composition is unlike any known solar system material. We compare these compositions to known differentiated bodies in the solar system and find them similar to those of evolved planetary materials–with lunar KREEP the closest in terms of its trace element enrichment pattern, but unusual in terms of their elevated CI-normalized incompatible elements. The “BeLaU”-type spherules reflect a highly differentiated, extremely evolved composition of an unknown source.

Genome-Wide Mapping of Main Histone Modifications and Coordination Regulation of Metabolic Genes under Salt Stress in Pea (Pisum sativum L)

Abstract Pea occupy a key position in modern biogenetics, playing a multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2 and the transcriptome in pea under normal condition, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across approximately 82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

Characterization and spatial distribution of infiltrating lymphocytes in medullary, and lymphocyte-predominant triple negative breast cancers

Medullary carcinoma of the breast (MedBC) is a rare histological type that accounts for less than 5% of all invasive breast cancers. Here, we performed an exploratory study aimed to determine whether imaging mass cytometry (IMC) can be used to characterize the immune infiltration and the spatial distribution heterogeneity in the rare subtype of MedBC compared to atypical MedBC and TNBC-TILS+ tumors. In both MedBC and TNBC-TILs+, there was a notable enrichment of immune cells in the peripheral regions of the tumors, whereas in atypical MedBC, the immune cells exhibited a central enrichment pattern. This distribution of infiltrated cells reflects an active immune recruitment correlated to more favorable prognosis. In MedBC, spatial analysis shows that immune cells are localized at a greater distance from the tumor cells. IMC highlights the heterogeneity of immune microenvironment across three main subtypes of breast tumors and could help to define distinct immune patterns.

Comparison of cat stone matrix and cat urine proteomes to human calcium oxalate stone matrix and urine proteomes.

Cat calcium oxalate monohydrate kidney stone matrix proteome showed great similarity to human calcium oxalate monohydrate stone matrix proteome, but inference of mechanistic similarity was limited by the absence of cat urine proteomic data. In this study, urine proteome distributions were measured by the same methods in 7 healthy cats for comparison to both the published human urine and cat calcium oxalate stone matrix proteomes to assess for similar enrichment patterns in both species. Furthermore, proteomic distributions were determined in cat struvite stone matrix to test for similarity to calcium oxalate monohydrate stone matrix and urine proteomes. Cat urine proteins demonstrated a similar distribution of abundance as a function of isoelectric points or net charge to human urine samples, and consequently the similarly altered patterns of protein distributions seen in calcium oxalate monohydrate stone matrix seen from both cat and human stones likely derives from the same preferential adsorption mechanism. Furthermore, the fact that protein abundance patterns seen in cat struvite stone matrix samples differ from both urine and calcium oxalate monohydrate stone matrix proteomes in systematic ways suggests that a combination of protein-protein and protein crystal interactions underly the formation of the crystal aggregates that comprise stones.

Unique Signatures of Highly Constrained Genes Across Publicly Available Genomic Databases.

Publicly available genomic databases and genetic constraint scores are crucial in understanding human population variation and the identification of variants that are likely to have a deleterious impact causing human disease. We utilized the one of largest publicly available databases, gnomAD, to determine genes that are highly constrained for only LoF, only missense, and both LoF/missense variants, identified their unique signatures, and explored their causal relationship with human conditions. Those genes were evaluated for unique patterns including their chromosomal location, tissue level expression, gene ontology analysis, and gene family categorization using multiple publicly available databases. Those highly constrained genes associated with human disease, we identified unique patterns of inheritance, protein size, and enrichment in distinct molecular pathways. In addition, we identified a cohort of highly constrained genes that are currently not known to cause human disease, that we suggest will be candidates to pursue as novel disease-associated genes. In summary, these insights not only elucidate biological pathways of highly constrained genes that expand our understanding of critical cellular proteins but also advance research in rare diseases.

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

New genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic impacts and evolutionary patterns over time remain elusive in humans due to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, our research shows a gradual rise in disease gene proportion as gene age increases. Logistic regression modeling indicates that this increase in older genes may be related to their longer sequence lengths and higher burdens of deleterious de novo germline variants (DNVs). We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a pleiotropy-barrier model that delineates higher potentials for phenotypic innovation in young genes compared to older genes, a process that is subject to natural selection. Our study demonstrates that evolutionarily new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.

Olfr2-positive macrophages originate from monocytes proliferate in situ and present a pro-inflammatory foamy-like phenotype.

Olfactory receptor 2 (Olfr2) has been identified in a minimum of 30% of vascular macrophages, and its depletion was shown to reduce atherosclerosis progression. Mononuclear phagocytes, including monocytes and macrophages within the vessel wall, are major players in atherosclerosis. Single-cell RNA sequencing studies revealed that atherosclerotic artery walls encompass several monocytes and vascular macrophages, defining at least nine distinct subsets potentially serving diverse functions in disease progression. This study investigates the functional phenotype and ontogeny of Olfr2-expressing vascular macrophages in atherosclerosis. Olfr2+ macrophages rapidly increase in Apoe-/- mice's aorta when fed a Western diet (WD). Mass cytometry showed that Olfr2+ cells are clustered within the CD64 high population and enriched for CD11c and Ccr2 markers. Olfr2+ macrophages express many pro-inflammatory cytokines, including Il1b, Il6, Il12, and Il23, and chemokines, including Ccl5, Cx3cl1, Cxcl9, and Ccl22. By extracting differentially expressed genes from bulk RNA sequencing (RNA-seq) of Olfr2+ vs. Olfr2- macrophages, we defined a signature that significantly mapped to single-cell data of plaque myeloid cells, including monocytes, subendothelial MacAir, and Trem2Gpnmb foamy macrophages. By adoptive transfer experiments, we identified that Olfr2 competent monocytes from CD45.1Apoe-/-Olfr2+/+ mice transferred into CD45.2Apoe-/-Olfr2-/- recipient mice fed WD for 12 weeks, accumulate in the atherosclerotic aorta wall already at 72 h, and differentiate in macrophages. Olfr2+ macrophages showed significantly increased BrdU incorporation compared to Olfr2- macrophages. Flow cytometry confirmed that at least 50% of aortic Olfr2+ macrophages are positive for BODIPY staining and have increased expression of both tumour necrosis factor and interleukin 6 compared to Olfr2- macrophages. Gene set enrichment analysis of the Olfr2+ macrophage signature revealed a similar enrichment pattern in human atherosclerotic plaques, particularly within foamy/TREM2hi-Mφ and monocytes. In summary, we conclude that Olfr2+ macrophages in the aorta originate from monocytes and can accumulate at the early stages of disease progression. These cells can undergo differentiation into MacAir and Trem2Gpnmb foamy macrophages, exhibiting proliferative and pro-inflammatory potentials. This dynamic behaviour positions them as key influencers in shaping the myeloid landscape within the atherosclerotic plaque.

Helium resources accumulation regulations and their development prospects in China

Helium is a globally scarce strategic resource that is relevant to national economies and the development of high-tech industries, and China primarily depends on imported helium for its industrial applications. Therefore, there is an urgent demand for clarifying helium formation and enrichment patterns, searching for helium-rich fields, and realizing China's helium resource inventory and development potential. This article analyzes the reservoir characteristics and accumulation conditions of typical helium-rich fields in China, and clarifying the origin and source of helium as well as the main controlling factors of helium enrichment. It was recognized that helium in natural gas in China mainly comes from crustal sources. Relatively shallow buried ancient U–Th-rich granite basement or intrusion, large and stable ancient uplift or submarine formed in the early period, good overburden of huge thick paste-salt rock or mudstone cover, and channels connecting the basement and reservoir, were the main controlling factors of helium enrichment. Four types of helium-rich gas reservoirs, namely helium-rich conventional gas, helium-rich shale gas, helium-rich non-hydrocarbon gas, and helium-rich water-soluble gas, have been modeled and predicted to be helium-rich favorable exploration areas. Based on this analysis, the prospect of helium resource development in China has been analyzed. It was proposed that the exploration of helium-rich fields and the comprehensive development and utilization of medium- and low-abundance helium resources are important ways to increase the domestic helium production in China in the future.

Identification of transcription factor co-binding patterns with non-negative matrix factorization.

Transcription factor (TF) binding to DNA is critical to transcription regulation. Although the binding properties of numerous individual TFs are well-documented, a more detailed comprehension of how TFs interact cooperatively with DNA is required. We present COBIND, a novel method based on non-negative matrix factorization (NMF) to identify TF co-binding patterns automatically. COBIND applies NMF to one-hot encoded regions flanking known TF binding sites (TFBSs) to pinpoint enriched DNA patterns at fixed distances. We applied COBIND to 5699 TFBS datasets from UniBind for 401 TFs in seven species. The method uncovered already established co-binding patterns and new co-binding configurations not yet reported in the literature and inferred through motif similarity and protein-protein interaction knowledge. Our extensive analyses across species revealed that 67% of the TFs shared a co-binding motif with other TFs from the same structural family. The co-binding patterns captured by COBIND are likely functionally relevant as they harbor higher evolutionarily conservation than isolated TFBSs. Open chromatin data from matching human cell lines further supported the co-binding predictions. Finally, we used single-molecule footprinting data from mouse embryonic stem cells to confirm that the COBIND-predicted co-binding events associated with some TFs likely occurred on the same DNA molecules.

Extra-terrestrial mantle samples: Rare Earth Element variations and evidence for melt metasomatism in ureilite meteorites

Ureilites are meteorites derived from the mantle of a reduced differentiated asteroid, the “Ureilite Parent Body” (UPB), which was later disrupted by impact with another Solar System body. They have ultramafic compositions dominated mostly by olivine and pigeonite with rare orthopyroxene and augite; aluminous phases are generally absent. Ureilites vary from abundant peridotites to much rarer pyroxenites, and their core olivine compositions range from Fo74 to Fo97 across different samples. The UPB experienced sufficiently high temperatures to undergo silicate partial melting, as shown by depletion in the Light Rare Earth Elements (LREE) in bulk restitic ureilites. Plagioclase and merrillite were probably present in the UPB mantle but have been completely removed during silicate partial melting. Partial melts of the UPB mantle are represented by glassy melt inclusions, igneous clasts in ureilite breccias, cumulus augite in some ureilites, and rare trachyandesitic fragments. These melts are generally intermediate and sub-alkaline in composition, although a few are alkaline. They have more enriched and flatter bulk REE patterns than the restitic ureilites and often show positive Eu anomalies. Glasses (representing melts) in ureilites from this study range from 57 to 79 wt% SiO2. One sample (AhS 22) shows petrographic and geochemical evidence for interaction between magma and the solid UPB mantle by forming metasomatic augite.Silicate minerals in ureilites analysed by LA-ICP-MS are generally LREE-depleted, with negative Eu anomalies. Ureilitic olivines have the lowest REE contents and the smallest negative Eu anomalies. Low-Ca pyroxenes have similar patterns with slightly stronger Eu anomalies. Augites have the highest REE contents and the most negative Eu anomalies. Augites show REE disequilibrium with olivine and low-Ca pyroxene, suggesting that they were not part of the restitic assemblage but were added by silicate melts passing through the UPB mantle, i.e. they are metasomatic in origin. We also discuss the size of the original UPB, using silicate minerals as evidence for it being a typical asteroid rather than a planet-sized object.

Machine Learning Uncovers Vascular Endothelial Cell Identity Genes by Expression Regulation Features in Single Cells.

Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and many diseases involving cell identity dysregulation. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes are regulated with unique epigenetic signatures, we found cell identity genes exhibit distinctive genetic sequence signatures, e.g., unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, enables SCIG to uncover the identity genes of a cell without a need for comparison to other cells. Cell identity gene score defined by SCIG surpassed expression value in network analysis to uncover master transcription factors regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master transcription factors for cell identity refinement. SCIG is publicly available at https://github.com/kaifuchenlab/SCIG , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.

Tandem mass tag (TMT)-based quantitative proteomics analysis reveals the different responses of contrasting alfalfa varieties to drought stress

BackgroundDrought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs).ResultsIn total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were ‘Translation, ribosomal structure and biogenesis’ and ‘Posttranslational modification, protein turnover, chaperones’. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in ‘photosynthesis’ and ‘ribosome’. The pathways of ‘linoleic acid metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘RNA transport’ in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment.ConclusionsThe differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Trace metals in coastal marine sediments: Natural and anthropogenic sources, correlation matrices, and proxy potentials

Rapidly spreading industrialization since the 19th century has led to a drastic increase in trace metal deposition in coastal sediments. Provided that these trace metals have remained relatively immobile after deposition, their sedimentary enrichments can serve as records of local–regional pollution histories. Factors controlling this proxy potential include trace metal geochemistry (carrier-, and host phase affinity), and depositional environmental factors (redox variability, particulate shuttling, organic matter loading, bathymetry). Yet, the relative importance and interactions between these controls are still poorly understood, hampering the reliable use of trace metal-based environmental proxies. By summarizing nine site-specific correlation matrices of 16 metal (loid) s (Pb, Cd, Cu, Zn, Sb, Sn, Ni, As, Tl, V, Mo, U, Re, Fe, Mn, Al), total organic C, and S contents in short sediment cores into a single meta-matrix, we test a novel approach for quickly detecting common and contrasting trace metal enrichment patterns across different study locations. Our meta-matrix shows two trace metal groups, within which positive correlations of e.g., Pb, Cd, Zn, Cu, Sb suggest a primary “anthropogenically sourced” (group I) control, whereas known “redox-sensitive” (group II) trace metals (Mo, U, Re) are characterized by fewer positive correlations. However, some group I metals (Cd, Zn, Cu, Sb) also covary with group II metals, inferring that redox variability may obscure primary anthropogenic signals; Sb even shows advantages over Mo and U under oxic conditions. As a more robust pollution indicator we identified Pb; yet for reconstructing historical Pb atmospheric pollution signals (1970s Pb peak), it is crucial to consider the distance from shore. In near-shore environments, local (fluvial) pollution signals may overprint large-scale (atmospheric) signals. Our findings demonstrate that combining site-specific sedimentary correlation and distribution patterns with a meta-matrix considerably aids the understanding of trace metal sequestration in different coastal sedimentary environments, which thereby improves trace metal proxy reliability.

Evaluating seasonal variation in macronutrient levels and their impact on water quality in urban coastal waters: A case study in nutrient management along the North Colombo coast of Sri Lanka

Macronutrients are vital for sustaining marine food webs and primary production. However, their overabundance through riverine inflows and untreated wastewater discharges causes adverse ecological changes, especially in developing countries, necessitating effective nutrient management for ecosystem preservation. We assessed macronutrient enrichment and dispersion patterns in the north Colombo coast of Sri Lanka, an urban estuary stressed by untreated wastewater discharge from sewer channels and macronutrients from the Kelani River. Maximum concentrations of NO3−−N, total dissolved nitrogen, PO43−−P and total dissolved phosphorus were 0.085, 0.74, 0.70, and 0.79 mg/L, respectively, while the dissolved oxygen levels and temperature ranged from 6.42 to 8.62 mg/L and from 28.1 to 30.8 0C during January 2023. The estuary was a nitrogen-limited ecosystem, with the Kelani River being the primary source of NO3−−N. Although nutrient levels were within water quality guidelines, understanding how pollutants disperse during a catastrophic discharge is crucial for risk management. Simulated dispersion patterns using Delft3D revealed that NO3−−N and other solutes introduced through the Kelani River accumulate near the breakwaters of the Colombo harbor complex during the Northeast monsoon, primarily due to seasonal wave and wind conditions. The accumulation of the limiting nutrient increased the risk of eutrophication and harmful algal blooms by non-indigenous toxic algae species introduced by untreated ballast water disposal. The findings elucidate the critical role of breakwaters in retaining solutes and emphasize the influence of morphological, climatic, and topographical factors on dispersion patterns in coastal ecosystems. The study provides an example for developing countries to integrate cost-effective monitoring technologies and numerical modelling into coastal management, facilitating data-driven decision making for effective environmental management.

Natural Enrichment Patterns and Mechanisms of Heavy Metals in Mid-Holocene Soils of the Southern Loess Plateau

Natural Enrichment Patterns and Mechanisms of Heavy Metals in Mid-Holocene Soils of the Southern Loess Plateau

Analysis of Carboniferous‐Permian coal‐accumulating environment and coalbed methane enrichment in the southern Qinshui Basin

Global research on the geological particularities of coal‐accumulating environments and the enrichment patterns of coalbed methane (CBM) is still relatively weak. This paper studies the geological characteristics and coal accumulation patterns of Carboniferous‐Permian coal‐bearing seams in the southern Qinshui Basin. The results show that the coal‐bearing strata in the basin represent the offshore marine and continental intercalated coal seam sediments developed. The southern part of the basin is dominated by lacustrine facies, and the delta front sub‐facies is locally developed. The characteristics of coal accumulation environment in the southern Qinshui Basin are characterized by basement properties, fault networks and coal‐bearing sedimentary facies, which collectively control the spatial and temporal distribution characteristics of the coal‐rich belt. The differences in coal accumulation environment in the southern basin affect the tectonic evolution, the thickness of the coal seam roof and floor and the hydrogeological conditions of the coal‐rich area, which further control the CBM enrichment in the Taiyuan‐Shanxi Formation. The aim of this study is to explore the factors of CBM enrichment and gas control mode, so as to enrich and improve the theory and method of CBM exploration, which will also help identify the appropriate underground geological structure environment for carbon sequestration (CCS), reduce greenhouse gas emissions and effectively respond to the challenge of global warming.

The new region demarcation framework for implementing the joint prevention and control of groundwater pollution: A case study in western of Bohai Bay, China

The joint groundwater pollution prevention and control (GPPC) strategy has been extensively implemented to address the coastal region groundwater pollution challenges in China. However, regional groundwater pollution control and treatment efficiency cannot achieve the expected results due to the lack of regional priority control orders and accurate restoration levels. Thus, this study developed a new region demarcation framework method for delineating GPPC zones, in tandem with a comprehensive pollution index method, the DRASTIC model, source apportionment. To validate the new methodological framework, a case study of groundwater pollution in Qinhuangdao, the western of Bohai Bay, China, was implemented to calculate pollution prevention and control zoning. In total, 340 groundwater samples from shallow aquifers with 9 target pollutants (NO3-, NO2-, NH4+, As, Cd, Cr, Cu, Pb, and Ni) were selected as the dataset for GPPC regionalization. The results showed that GPPC zoning further clarified the direction of groundwater pollution protection and management in Qinhuangdao. Compared to the traditional method, the new GPPC zoning better reflects groundwater mobility characteristics and pollution transport and enrichment patterns in terms of groundwater functional integrity and delineation. This new regional demarcation framework method contributes to providing support for the fine division of groundwater pollution zoning and precise pollution control for groundwater resource management in China.

Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.).

Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency.

Comparative quantitative phosphoproteomic and parallel reaction monitoring analysis of soybean roots under aluminum stress identify candidate phosphoproteins involved in aluminum resistance capacity

Aluminum (Al) toxicity adversely impacts soybean (Glycine max) growth in acidic soil. Reversible protein phosphorylation plays an important role in adapting to adverse environmental conditions by regulating multiple physiological processes including signal transduction, energy coupling and metabolism adjustment in higher plant. This study aimed to reveal the Al-responsive phosphoproteins to understand their putative function and involvement in the regulation of Al resistance in soybean root. We used immobilized metal affinity chromatography to enrich the key phosphoproteins from soybean root apices at 0, 4, or 24 h Al exposure. These phosphoproteins were detected using liquid chromatography-tandem mass spectrometry measurement, verified by parallel reaction monitoring (PRM), and functionally characterized via overexpression in soybean hairy roots. A total of 638 and 686 phosphoproteins were identified as differentially enriched between the 4-h and 0-h, and the 24-h and 0-h Al treatment comparison groups, respectively. Typically, the phosphoproteins involved in biological processes including cell wall modification, and RNA and protein metabolic regulation displayed patterns of decreasing enrichment (clusters 3, 5 and 6), however, the phosphoproteins involved in the transport and metabolic processes of various substrates, and signal transduction pathways showed increased enrichment after 24 h of Al treatment. The enrichment of phosphoproteins in organelle organization bottomed after 4 h of Al treatment (cluster 1). Next, we selected 26 phosphoproteins from the phosphoproteomic profiles, assessed their enrichment status using PRM, and detected enrichment patterns similar to those observed via phosphoproteomic analysis. Among them, 15 phosphoproteins were found to reduce the accumulation of Al and callose in Al-stressed soybean root apices when their corresponding genes were individually overexpressed in soybean hairy roots. In summary, the findings of this study facilitated a comprehensive understanding of the protein phosphorylation events involved in Al resistance responses and revealed some critical phosphoproteins that enhance Al resistance in soybean roots.