Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.

Mapping the cell phylogeny of a complex multicellular organism relies on somatic mutations accumulated from zygote to adult. Available cell barcoding methods can record about three mutations per barcode, enabling only low-resolution mapping of the cell phylogeny of complex organisms. Here we developed SMALT, a substitution mutation-aided lineage-tracing system that outperforms the available cell barcoding methods in mapping cell phylogeny. We applied SMALT to Drosophila melanogaster and obtained on average more than 20 mutations on a three-kilobase-pair barcoding sequence in early-adult cells. Using the barcoding mutations, we obtained high-quality cell phylogenetic trees, each comprising several thousand internal nodes with 84-93% median bootstrap support. The obtained cell phylogenies enabled a population genetic analysis that estimates the longitudinal dynamics of the number of actively dividing parental cells (Np) in each organ through development. The Np dynamics revealed the trajectory of cell births and provided insight into the balance of symmetric and asymmetric cell division.

A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants.

CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.

Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis.

Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.

Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China.

The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.

Systematic study of tissue section thickness for MALDI MS profiling and imaging.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) has become a powerful method for studying the spatial distribution of molecules. Preparation of tissue sections is a critical step for obtaining high-quality imaging data. The thickness of the slice of tissue affects the feature quality of MALDI MSI. However, few studies involved in-depth and systematic examination of slice thickness. Herein, we investigate the effect of tissue slice thickness on MALDI MSI detection. We found that the thicker the slice, the worse the results obtained by MALDI MS, which we attributed to the charging effect. The optimal slice thickness of brain tissue obtained in this work is 2-6 µm. Comparisons of the effects of slice thickness on atmospheric pressure and vacuum MALDI assays indicated that the ion signals and imaging quality of vacuum MALDI were more seriously affected by the thickness, with atmospheric pressure (AP) MALDI having a greater tolerance for slice thickness than vacuum MALDI. The MALDI MSI of peptides after enzymatic digestion of tissue sections of different thicknesses was also studied, revealing that the most suitable tissue thickness for enzyme digestion is about 10 µm. Finally, we optimized the slice thicknesses of six tissues in mice to provide a reference for MALDI MSI studies. It is worth mentioning that in our study the values of slice thickness range from the nanometer level (400 nm) at the minimum to 150 µm at the maximum, values which were unprecedented. Detailed in-depth and systematic studies of slice thickness will promote the development of sample preparation technology of AP and vacuum MALDI MSI, which will provide important references for the selection of tissue section thickness.

Comparative study on plant growth-promoting bacterial inoculation by irrigation and spraying for promoting Bidens pilosa L. phytoremediation of cadmium-contaminated soil.

A field study was conducted to compare FM-1 inoculation by irrigation and spraying for promoting Bidens pilosa L. phytoremediation of cadmium (Cd)-contaminated soil. Cascading relationships between bacterial inoculation by irrigation and spraying and soil properties, plant growth-promoting traits, plant biomass and Cd concentrations in Bidens pilosa L. were explored based on the partial least squares path model (PLS-PM). The results indicated that inoculation with FM-1 not only improved the rhizosphere soil environment of B. pilosa L. but also increased the Cd extracted from the soil. Moreover, Fe and P in leaves play vital roles in promoting plant growth when FM-1 is inoculated by irrigation, while Fe in leaves and stems plays a vital role in promoting plant growth when FM-1 is inoculated by spraying. In addition, FM-1 inoculation decreased the soil pH by affecting soil dehydrogenase and oxalic acid in cases with irrigation and Fe in roots in cases with spraying. Thus, the soil bioavailable Cd content increased and promoted Cd uptake by Bidens pilosa L. To address Cd-induced oxidative stress, Fe in leaves helped to convert GSH into PCs, which played a vital role in ROS scavenging when FM-1 was inoculated by irrigation. The soil urease content effectively increased the POD and APX activities in the leaves of Bidens pilosa L., which helped alleviate Cd-induced oxidative stress when FM-1 was inoculated by spraying. This study compares and illustrates the potential mechanism by which FM-1 inoculation can improve the phytoremediation of Cd-contaminated soil by Bidens pilosa L., suggesting that FM-1 inoculation by irrigation and spraying is useful in the phytoremediation of Cd-contaminated sites.

Global perspectives for biochar application in the remediation of heavy metal-contaminated soil: a bibliometric analysis over the past three decades.

Herein, 7,308 relevant documents on biochar application for the remediation of heavy metal (HM)-contaminated soil (BARHMCS) from 1991 to 2020 were extracted from the Web of Science Core Collection and subjected to bibliometric and knowledge mapping analyses to provide a global perspective. The results showed that (1) the number of publications increased over time and could be divided into two subperiods, i.e., the slow growth period (SGP) and rapid growth period (RGP), according to whether the annual publication number was ≥300. (2) A total of 126 countries, 741 institutions, and 1,021 scholars have contributed to this field. (3) These studies are mainly published in Science of the Total Environment, Chemosphere, etc., and are mainly based on the categories of environmental science, soil science, and environmental engineering. (4) The top five keyword clusters for the SGP were biochar, biochar, sorption, charcoal, and HMs, and those for the RGP were adsorption, black carbon, nitrous oxide, cadmium, and pyrolysis. (5) The main knowledge domains and the most cited references during the SGP and RGP were discussed. (6) Future directions are related to biochar application for plant remediation, the mitigation of climate change through increased carbon sequestration, biochar modification, and biochar for HMs and multiple organic pollutants.

Biochar application in the remediation of heavy metal-contaminated soil (BARHMCS) has become a popular research topic worldwide. Many excellent papers on this topic have been published, including some valuable reviews. However, there are no reviews including bibliometric and visual analyses. In the present study, bibliometric and visual analyses of relevant literature in the field of BARHMCS based on the Web of Science Core Collection were carried out to outline the development process of this field at a macro level, clarify the research hotspots, identify the knowledge domains that support this field, and explore future research directions. These efforts will no doubt help readers fully understand BARHMCS from a global perspective and provide a reference for future research. HIGHLIGHTSAn overall global perspective of biochar remediation of heavy metal (HM)-contaminated soil was provided.The main popular research topics of each period were discussed.Knowledge domains were discussed.Five main future research directions were identified based on burst keyword analysis.Biochar modification and its effect on HMs and coexisting organic pollutants should be studied in the future for soil remediation purposes.

Plant growth and heavy meal accumulation characteristics of Spathiphyllum kochii cultured in three soil extractions with and without silicate supplementation.

A hydroponic method was conducted to test whether Spathiphyllum kochii is tolerant to multiple HMs as well as to evaluate whether sodium silicate promotes plant growth and alleviates HM stress mainly by assessing biomass, HM accumulation characteristics and antioxidant enzyme activities (AEAs). Three soil extractions from an uncontaminated soil, a comparable lightly HM-contaminated soil (EnSE), and a comparable heavily HM-contaminated soil (ExSE) with or without 1 mM sodium silicate supplementation were used. S. kochii showed no obvious symptoms when cultured in EnSE and ExSE, indicating that it was a multi-HM-tolerant species. The biomass and photosynthesis followed the order: UnSE > EnSE > ExSE, but the opposite order was found for HM concentration, AEAs, and malondialdehyde content. Silicate had no effects on the growth and HM bioaccumulation characteristics of S. kochii cultured in UnSE but exhibited a novel role in decreasing HM uptake by 13.61-41.51% in EnSE and ExSE, respectively, corresponding upregulated AEAs, and reduced malondialdehyde contents, resulting in increased biomass and alleviating HM stress. The activities of peroxidase and superoxide dismutase were upregulated by an increase in soil extraction HM concentration and further upregulated by silicate supplementation, indicating that they were important mechanisms alleviating HM stress in S. kochii.

Phytoremediation is an economical and environmentally friendly technology for the alleviation of heavy metal (HM)-contaminated soil. Improving bioremediation efficiency is crucial for this kind of technology. Many studies have shown that silicon plays a novel role in plant growth and adversity responses, but studies in the field of phytoremediation are limited. In addition, phytoremediation plant species are usually hyperaccumulators or may be tolerant crops, commercial crops, or wild species from mining areas, and the use of landscape species in phytoremediation is limited. This is the first report on the effects of silicate on the multi-HM bioaccumulation characteristics of a garden plant (Spathiphyllum kochii) cultured in uncontaminated and HM-contaminated soil extractions. This study will broaden phytoremediation species screening and enrich our understanding of the mechanisms by which Si supports the bioremediation of HM-contaminated environments.HIGHLIGHTSS. kochii was a multi-heavy metal-tolerant species.Silicon played a novel role in reducing heavy metal concentrations by 14­40% and 14­42% in shoots and roots, respectively.Silicon upregulated antioxidant enzyme activities to alleviate heavy metal stress in plants.

CaFe-layered double hydroxide corn straw biochar reduced heavy metal uptake by Brassica campestris L. and Ipomoea aquatic F.: Rhizosphere effects and oxidative stress alleviation.

In the present study, CaFe-layered double hydroxide corn straw biochar (CaFe-LDH@CSB) was applied to the rhizosphere soil of both pakchoi (Brassica campestris L. ssp. Chinensis Makino, B. campestris L.) and water spinach (Ipomoea aquatic F., I. aquatic F.) to explore and clarify the potential mechanism by which CaFe-LDH@CSB helps vegetables reduce heavy metal (HM) uptake and alleviate oxidative stress. Pot experiments were conducted with CaFe-LDH@CSB applied at four levels: control (CK), T1 (5 g kg-1), T2 (10 g kg-1) and T3 (20 g kg-1). The results indicated that the application of CaFe-LDH@CSB significantly increased pH and decreased the acid-soluble forms of Cd, Pb, Zn and Cu in the rhizosphere soil of both B. campestris L. and I. aquatic F.; decreases of 39.4%, 18.0%, 10.0% and 33.3% in B. campestris L. and of 26.6%, 49.1%, 13.2% and 36.8% in I. aquatic F., respectively, were observed at the T3 level. Moreover, CaFe-LDH@CSB application reduced HM uptake by B. campestris L. and decreased HM-induced oxidative stress through the regulation of soil physicochemical properties and microbial abundance. For B. campestris L., variations in Sordariomycetes helped alleviate the accumulation of HMs in the aerial part, while GSH and -SH from the nonenzymatic system played an important role in scavenging H2O2 in leaves, thus helping B. campestris L. alleviate HM-induced oxidative stress. For I. aquatica F., variations in Vicinamibacteria and Mortierellomycetes helped alleviate the accumulation of HMs in plants, while GSH and PCs from nonenzymatic systems played an important role in removing ·O2- in leaves, thereby helping I. aquatica F. alleviate HM-induced oxidation stress. Our study indicated that the application of CaFe-LDH@CSB improved the rhizosphere soil environment and rebuilt the soil microbial community, helping B. campestris L. and I. aquatica F. alleviate HM-induced oxidative stress and promoting the growth of both vegetables.

Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine.

Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH4+-N and NO3--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.

Screening of radiation gastrointestinal injury biomarkers in rat plasma by high-coverage targeted lipidomics.

INTRODUCTION: In the event of radiological accidents and cancer radiotherapies in the clinic, the gastrointestinal (GI) system is vulnerable to ionizing radiation and shows GI injury. Accessible biomarkers may provide means to predict, evaluate, and treat GI tissue damage. The current study investigated radiation GI injury biomarkers in rat plasma. MATERIAL AND METHODS: High-coverage targeted lipidomics was employed to profile lipidome perturbations at 72 h after 0, 1, 2, 3, 5, and 8 Gy (60Co γ-rays at 1 Gy/min) total-body irradiation in male rat jejunum. The results were correlated with previous plasma screening outcomes. RESULTS: In total, 93 differential metabolites and 28 linear dose-responsive metabolites were screened in the jejunum. Moreover, 52 lipid species with significant differences both in jejunum and plasma were obtained. Three lipid species with linear dose-response relationship both in jejunum and plasma were put forth, which exhibited good to excellent sensitivity and specificity in triaging different exposure levels. DISCUSSION: The linear dose-effect relationship of lipid metabolites in the jejunum and the triage performance of radiation GI injury biomarkers in plasma were studied for the first time. CONCLUSION: The present study can provide insights into expanded biomarkers of IR-mediated GI injury and minimally invasive assays for evaluation.

AL amyloidosis with primary presentation of multiple serous cavity effusion and severe cholestasis: a case report and review of literature.

BACKGROUND: Immunoglobulin light chain (AL) amyloidosis commonly affects the kidney or heart, but may also involve the liver at a histopathological level. Early diagnosis of AL amyloidosis is important for proper management with desirable outcome. We reported here an unusual case of AL amyloidosis, presenting primarily with multiple serous cavity effusion, accompanied with rapidly progressive cholestasis. CASE PRESENTATION: A previously healthy 63-year-old man presented with dysuria, frequent urination, oliguria and oedema of lower extremities for one month, accompanied with jaundice and hypoproteinemia. CT demonstrated multiple serous cavity effusion, focal hypodense lesions in the liver, and focal low-density in the spleen. Laparoscopy with liver biopsy revealed liver and spleen fibrosis with congestion, no visceral rupture, following haemorrhagic ascites from abdominocentesis. This patient was transferred to our (tertiary) hospital. The diagnosis of amyloidosis was confirmed with histopathology/immunohistochemistry. Haematopoietic stem cell transplantation was not applicable, however chemotherapy was advised, due to the patient's Mayo score 3. The patient declined chemotherapy and was self-discharged back to his hometown hospital with palliative care, however only lasted a further one-month. DISCUSSION: The lesson we have learnt from this case that any patients with multiple serous cavity effusion and isolated hepatic involvement, primary amyloidosis should be considered. Multiple serous cavity effusion may serve as an indicator for poor prognosis of hepatic AL amyloidosis.

Bacterial extracellular polymeric substances: Impact on soil microbial community composition and their potential role in heavy metal-contaminated soil.

In this study, six different treatments involving extracellular polymeric substances (EPS) from Enterobacter sp. FM-1 (FM-1) (no EPS (control), original bacterial cells (FM-1), FM-1 cells with EPS artificially removed (EPS-free cells, EPS-R), different forms of EPS (soluble EPS (S-EPS), loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS)) obtained from FM-1) and three types of soils (non-contaminated soil (NC soil), high-contamination soil (HC soil) and low-contamination soil (LC soil)) were used to investigate the impact of different EPS treatments on soil microbial community composition and their potential role in the remediation of heavy metal (HM)-contaminated soil. The results indicate that the EPS secreted by FM-1 played a vital role in changing soil pH and helped increase soil bio- HMs. In addition, EPS secretion by FM-1 helped increase the soil EPS-polysaccharide and EPS-nucleic acid contents; even in HC soil, where the HM content was relatively high, LB-EPS addition still increased the EPS-polysaccharide and EPS-nucleic acid contents in the soil by 1.18- and 15.54-fold, respectively. FM-1, LB-EPS and TB-EPS addition increased the soil invertase, urease and alkaline phosphatase activities and increased the soil organic matter (SOM), NH4+-N and available phosphorus (AP) contents, which helped regulate soil nutrient reserves. Moreover, the addition of different EPS fractions modified the soil microbial community composition to help microbes adapt to an HM-contaminated environment. In the HC and LC soils, where the HM content was relatively high, the soil bacteria were dominated by Protobacteria, while fungi in the soil were dominated by Ascomycota. Among the soil physicochemical properties, the soil SOM and NH4+-N contents and invertase activity significantly impacted the diversity and community composition of both bacteria and fungi in the soil.

Screening of Lipids for Early Triage and Dose Estimation after Acute Radiation Exposure in Rat Plasma Based on Targeted Lipidomics Analysis.

Rapid early triage and dose estimation is vital for limited medical resource allocation and treatment of a large number of the wounded after radiological accidents. Lipidomics has been utilized to delineate biofluid lipid signatures after irradiation. Here, high-coverage targeted lipidomics was employed to screen radiosensitive lipids after 0, 1, 2, 3, 5, and 8 Gy total body irradiation at 4, 24, and 72 h postirradiation in rat plasma. Ultra-performance liquid chromatography-tandem mass spectrometry with a multiple reaction monitoring method was utilized. In total, 416 individual lipids from 18 major classes were quantified and those biomarkers altered in a dose-dependent manner constituted panel A-panel D. Receiver operator characteristic curve analysis using combined lipids showed good to excellent sensitivity and specificity in triaging different radiation exposure levels (area under curve = 0.814-1.000). The equations for dose estimation were established by stepwise regression analysis for three time points. A novel strategy for radiation early triage and dose estimation was first established and validated using panels of lipids. Our study suggests that it is feasible to acquire quantitative lipid biomarker panels using targeted lipidomics platforms for rapid, high-throughput triage, which can provide further insights in developing lipidomics strategies for radiation biodosimetry in humans.

A novel role of sulfate in promoting Mn phytoextraction efficiency and alleviating Mn stress in Polygonum lapathifolium Linn.

A hydroponic method was performed to explore the effects of sulfate supply on the growth, manganese (Mn) accumulation efficiency and Mn stress alleviation mechanisms of Polygonum lapathifolium Linn. Three Mn concentrations (1, 8 and 16 mmol L-1, representing low (Mn1), medium (Mn8) and high (Mn16) concentrations, respectively) were used. Three sulfate (S) levels (0, 200, and 400 µmol L-1, abbreviated as S0, S200 and S400, respectively) were applied for each Mn concentration. (1) The average biomass (g plant-1) of P. lapathifolium was ordered as Mn8 (6.36) > Mn1 (5.25) > Mn16 (4.16). Under Mn16 treatment, S addition increased (P < 0.05) biomass by 29.96% (S200) and 53.07% (S400) compared to that S0. The changes in the net photosynthetic rate and mean daily increase in biomass were generally consistent with the changes in biomass. (2) Mn accumulation efficiency (g plant-1) was ordered as Mn8 (99.66) > Mn16 (58.33) > Mn1 (27.38); and S addition increased (p < 0.05) plant Mn accumulation and Mn transport, especially under Mn16 treatment. (3) In general, antioxidant enzyme activities (AEAs) and malondialdehyde (MDA) in plant leaves were ordered in Mn16 > Mn8 > Mn1. Sulfate addition decreased (P < 0.05) AEAs and MDA under Mn16 treatment, while the changes were minor under Mn1 and Mn8 treatments. (4) Amino acid concentrations generally increased with increasing Mn concentration and S level. In summary, the medium Mn treatment promoted plant growth and Mn bioaccumulation; sulfate, especially at 400 µmol L-1 S, can effectively promote plant growth and Mn accumulation efficiency. The most suitable bioremediation strategy was Mn16 with 400 µmol L-1 S.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area.

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the ß-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Bam-dependent deubiquitinase complex can disrupt germ-line stem cell maintenance by targeting cyclin A.

Drosophila germ-line stem cells (GSCs) provide an excellent model to study the regulatory mechanisms of stem cells in vivo. Bag of marbles (bam) has been demonstrated to be necessary and sufficient to promote GSC and cystoblast differentiation. Despite extensive investigation of its regulation and genetic functions, the biochemical nature of the Bam protein has been unknown. Here, we report that Bam is an ubiquitin-associated protein and controls the turnover of cyclin A (CycA). Mechanistically, we found that Bam associated with Otu to form a deubiquitinase complex that stabilized CycA by deubiquitination, thus providing a mechanism to explain how ectopic expression of Bam in GSCs promotes differentiation. Collectively, our findings not only identify a biochemical function of Bam, which contributes to GSC fate determination, but also emphasizes the critical role of proper expression of cyclin proteins mediated by both ubiquitination and deubiquitination pathways in balancing stem cell self-renewal and differentiation.

Membrane targeting of inhibitory Smads through palmitoylation controls TGF-ß/BMP signaling.

TGF-ß/BMP (bone morphogenetic protein) signaling pathways play conserved roles in controlling embryonic development, tissue homeostasis, and stem cell regulation. Inhibitory Smads (I-Smads) have been shown to negatively regulate TGF-ß/BMP signaling by primarily targeting the type I receptors for ubiquitination and turnover. However, little is known about how I-Smads access the membrane to execute their functions. Here we show that Dad, the Drosophila I-Smad, associates with the cellular membrane via palmitoylation, thereby targeting the BMP type I receptor for ubiquitination. By performing systematic biochemistry assays, we characterized the specific cysteine (Cys556) essential for Dad palmitoylation and membrane association. Moreover, we demonstrate that dHIP14, a Drosophila palmitoyl acyl-transferase, catalyzes Dad palmitoylation, thereby inhibiting efficient BMP signaling. Thus, our findings uncover a modification of the inhibitory Smads that controls TGF-ß/BMP signaling activity.

Comparative analysis of the seed germination of pakchoi and its phytoremediation efficacy combined with chemical amendment in four polluted soils.

The seed germination plant growth parameters and level of heavy metal accumulation were investigated in pakchoi cultured in four contaminated soils with different levels of heavy metals supplemented with citric acid (CA) or calcium phosphate (CP). Results showed that the seed germination energy, germination percentage and germination index parameters were similar, while the seed vigor (SV) significantly (p < 0.05) decreased as the soil pollution level increased. The lengths of the shoots and roots presented the same trend as SV. All the seedlings grew in heavily polluted soil without any amendments before harvesting; therefore, no plant material was available for subsequent analyses. The photosynthesis parameters of pakchoi cultured in lightly polluted soil without amendment (LPS), lightly polluted soil with CA (LPSA) and moderately polluted soil with CP (MPSP) were similar. The concentrations of Pb, Zn, Mn, Cu and Cd in the shoots, roots and whole plants were in the order of MPSP > LPSA > LPS. Pakchoi cultured in MPSP showed the most promising results in terms of plant height, biomass and heavy metal accumulation. Pakchoi presented the highest translocation and bioaccumulation factors for Cd and the lowest for Pb.HighlightsSoil pollution and the type of chemical amendment had no effect on the seed germination of pakchoi.Citric acid addition in lightly polluted soil improved pakchoi growth and heavy metal extraction.Pakchoi cultured in moderately polluted soil with calcium phosphate amendment presented the highest biomass and heavy metal concentration.

Manganese accumulation and plant physiology behavior of Camellia oleifera in response to different levels of potassium fertilization.

The effects of potassium (K) fertilization (KCl, analytically pure; 0, 60, 200, and 400 mg kg-1) on the growth and Mn accumulation of Camellia oleifera in two types of Mn-contaminated soils were investigated. The potential mechanisms underlying the impacts of K fertilization were explored. C. oleifera accumulated high amounts of Mn in both soil conditions. The addition of K fertilizer decreased the soil pH and promoted Mn accumulation in C. oleifera. However, the plant biomass decreased significantly under the high level of K fertilization (400 mg kg-1), and the oxidative stress was stimulated under Mn contamination. But an appropriate concentration of K fertilizer (200 mg kg-1) was necessary for the formation of photosynthesis pigments, nonenzymatic antioxidants and antioxidant enzymes, metabolic processes, and nutrient uptake. Furthermore, when plants supplemented with a low level of K fertilization (200 mg kg-1), the catalase activity in C. oleifera leaves was enhanced to alleviate oxidative stress and protect the plant from Mn contamination. Our study demonstrated that 200 mg kg-1 of K fertilizer has the potential to further enhance the efficiency of Mn phytoremediation by C. oleifera.