Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration.

Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.

Organelle Ca2+/CAM1-SELTP confers somatic cell embryogenic competence acquisition and transformation in plant regeneration.

Somatic cell totipotency in plant regeneration represents the forefront of the compelling scientific puzzles and one of the most challenging problems in biology. How somatic embryogenic competence is achieved in regeneration remains elusive. Here, we discover uncharacterized organelle-based embryogenic differentiation processes of intracellular acquisition and intercellular transformation, and demonstrate the underlying regulatory system of somatic embryogenesis-associated lipid transfer protein (SELTP) and its interactor calmodulin1 (CAM1) in cotton as the pioneer crop for biotechnology application. The synergistic CAM1 and SELTP exhibit consistent dynamical amyloplast-plasmodesmata (PD) localization patterns but show opposite functional effects. CAM1 inhibits the effect of SELTP to regulate embryogenic differentiation for plant regeneration. It is noteworthy that callus grafting assay reflects intercellular trafficking of CAM1 through PD for embryogenic transformation. This work originally provides insight into the mechanisms responsible for embryogenic competence acquisition and transformation mediated by the Ca2+/CAM1-SELTP regulatory pathway, suggesting a principle for plant regeneration and cell/genetic engineering.

Social Bonding, Risky Lifestyle, and Polyvictimization Among a Sample of Chinese Adolescents.

Polyvictimization has received substantial scholarly attention globally since it has been put forward two decades ago. However, the current lack of understanding of the causes of polyvictimization hinders the design of intervention programs. This study aims to integrate social bonding theory and lifestyle-routine activity theory to understand the etiology of polyvictimization in the Chinese context. Our results suggest that social bonding exerted not only a direct effect on polyvictimization (ß = -.030, p < .001) but also an indirect effect through delinquency and association with delinquent peers. Surprisingly, we found that the pathways linking social bonding and polyvictimization do not differ across genders. Implications for practice and theories are discussed.

GHG emissions and energy consumption of residential buildings-a systematic review and meta-analysis.

Residential buildings generate significant greenhouse gas (GHG) emissions and consume energy throughout their life cycle. In recent years, research on GHG emissions and energy consumption of buildings has developed rapidly in response to the growing climate change and energy crisis. Life cycle assessment (LCA) is an important method for evaluating the environmental impacts of the building sector. However, LCA studies of buildings show widely varying outcomes across the world. Besides, environmental impact assessment from a whole life cycle perspective has been undeveloped and slow. Our work presents a systematic review and meta-analysis of LCA studies on GHG emissions and energy consumption in the preuse, use, and demolition stages of residential buildings. We aim to examine the differences among the results of diverse case studies and demonstrate the spectrum of variations under contextual disparities. Results show that residential building emits about 2928 kg GHG emission and consumes about 7430 kWh of energy per m2 of gross building area on average throughout the life cycle. Residential buildings have an average GHG emission of 84.81% in the use phase, followed by the preuse phase and demolition phase; the mean energy consumption in the use stage occupied the largest share of 84.52%, followed by preuse stage and demolition stage. GHG emissions and energy use vary significantly in different regions due to different building types, natural conditions, and lifestyles. Our study stresses the compelling requirement to slash GHG emissions and optimize energy consumption from residential buildings by use of low carbon building materials, energy structure adjustment, consumer behavior transformation, etc.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.

Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

Ethyl methanesulfonate mutant library construction in Gossypium hirsutum L. for allotetraploid functional genomics and germplasm innovation.

As the gene pool is exposed to both strain on land resources and a lack of diversity in elite allotetraploid cotton, the acquisition and identification of novel alleles has taken on epic importance in facilitating cotton genetic improvement and functional genomics research. Ethyl methanesulfonate (EMS) is an excellent mutagen that induces genome-wide efficient mutations to activate the mutagenic potential of plants with many advantages. The present study established, determined and verified the experimental procedure suitable for EMS-based mutant library construction as the general reference guide in allotetraploid upland cotton. This optimized method and procedure are efficient, and abundant EMS mutant libraries (approximately 12 000) in allotetraploid cotton were successfully obtained. More than 20 mutant phenotypes were observed and screened, including phenotypes of the leaf, flower, fruit, fiber and plant architecture. Through the plants mutant library, high-throughput and high-resolution melting technology-based variation evaluation detected the EMS-induced site mutation. Additionally, based on overall genome-wide mutation analyses by re-sequencing and mutant library assessment, the examination results demonstrated the ideal quality of the cotton EMS-treated mutant library constructed in this study with appropriate high mutation density and saturated genome. What is more, the collection is composed of a broad repertoire of mutants, which is the valuable resource for basic genetic research and functional genomics underlying complex allotetraploid traits, as well as cotton breeding.

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton.

The somatic embryogenesis (SE) process of plants is regulated by exogenous hormones. During the SE, different genes sensitively respond to hormone signals through complex regulatory networks to exhibit plant totipotency. When cultured in indole-3-butyric acid (IBA) concentration gradient medium supplemented with 0 mg dm-3, 0.025 mg dm-3, and 0.05 mg dm-3 IBA, the callus differentiation rate first increased then decreased in cotton. To characterize the molecular basis of IBA-induced regulating SE, transcriptome analysis was conducted on embryogenic redifferentiation. Upon the examination of the IBA's embryogenic inductive effect, it was revealed that pathways related to plant hormone signal transduction and alcohol degradation were significantly enriched in the embryogenic responsive stage (5 days). The photosynthesis, alcohol metabolism and cell cycle pathways were specifically regulated in the pre-embryonic initial period (20 days). Upon the effect of the IBA dose, in the embryogenic responsive stage (5 days), the metabolism of xenobiotics by the cytochrome P450 pathway and secondary metabolism pathways of steroid, flavonoid, and anthocyanin biosynthesis were significantly enriched. The phenylpropanoid, brassinosteroid, and anthocyanin biosynthesis pathways were specifically associated in the pre-embryonic initial period (20 days). At different developmental stages of embryogenic induction, photosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, xenobiotics metabolism by cytochrome P450, and brassinosteroid biosynthesis pathways were enriched at low a IBA concentration. Meanwhile, at high IBA concentration, the carbon metabolism, alcohol degradation, circadian rhythm and biosynthesis of amino acids pathways were significantly enriched. The results reveal that complex regulating pathways participate in the process of IBA-induced redifferentiation in cotton somatic embryogenesis. In addition, collections of potential essential signaling and regulatory genes responsible for dose IBA-induced efficient embryogenic redifferentiation were identified. Quantitative real-time PCR (qRT-PCR) was performed on the candidate genes with different expression patterns, and the results are basically consistent with the RNA-seq data. The results suggest that the complicated and concerted IBA-induced mechanisms involving multiple cellular pathways are responsible for dose-dependent plant growth regulator-induced SE. This report represents a systematic study and provides new insight into molecular signaling and regulatory basis underlying the process of dose IBA-induced embryogenic redifferentiation during SE.

An H-ferritin from the hydrothermal vent shrimp Rimicaris exoculata and its potential role in iron metabolism.

Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species among hydrothermal vent communities along the Mid-Atlantic Ridge. This shrimp can tolerate high concentrations of heavy metals such as iron, but the mechanisms used for detoxification and utilization of excess metals remain largely unknown. Ferritin is a major iron storage protein in most living organisms. The central heavy subunit of ferritin (H-ferritin) possesses ferroxidase activity and converts iron from Fe2+ to Fe3+, the non-toxic form used for storage. In the present study, the H-ferritin RexFrtH was identified in the hydrothermal vent shrimp R. exoculata, and found to be highly expressed in the gill, the main organ involved in bioaccumulation of metals, at both RNA and protein levels. Accumulation of RexFrtH decreased from efferent to afferent vessels, coinciding with the direction of water flow through the gills. Fe3+ was localized with RexFrtH, and in vitro iron-binding and ferroxidase assays using recombinant RexFrtH confirmed the high affinity for iron. Based on these results, we propose a model of iron metabolism in R. exoculata gills; ferrous iron from ambient hydrothermal water accumulates and is converted and stored in ferric form by RexFrtH as an iron reservoir when needed for metabolism, or excreted as an intermediate to prevent iron overload. The findings expand our understanding of the adaptation strategies used by shrimps inhabiting extreme hydrothermal vents to cope with extremely high heavy metal concentrations.

Dynamic TMT-Based Quantitative Proteomics Analysis of Critical Initiation Process of Totipotency during Cotton Somatic Embryogenesis Transdifferentiation.

The somatic embryogenesis (SE) process of plants, as one of the typical responses to abiotic stresses with hormone, occurs through the dynamic expression of different proteins that constitute a complex regulatory network in biological activities and promotes plant totipotency. Plant SE includes two critical stages: primary embryogenic calli redifferentiation and somatic embryos development initiation, which leads to totipotency. The isobaric labels tandem mass tags (TMT) large-scale and quantitative proteomics technique was used to identify the dynamic protein expression changes in nonembryogenic calli (NEC), primary embryogenic calli (PEC) and globular embryos (GEs) of cotton. A total of 9369 proteins (6730 quantified) were identified; 805, 295 and 1242 differentially accumulated proteins (DAPs) were identified in PEC versus NEC, GEs versus PEC and GEs versus NEC, respectively. Eight hundred and five differentially abundant proteins were identified, 309 of which were upregulated and 496 down regulated in PEC compared with NEC. Of the 295 DAPs identified between GEs and PEC, 174 and 121 proteins were up- and down regulated, respectively. Of 1242 differentially abundant proteins, 584 and 658 proteins were up- and down regulated, respectively, in GEs versus NEC. We have also complemented the authenticity and accuracy of the proteomic analysis. Systematic analysis indicated that peroxidase, photosynthesis, environment stresses response processes, nitrogen metabolism, phytohormone response/signal transduction, transcription/posttranscription and modification were involved in somatic embryogenesis. The results generated in this study demonstrate a proteomic molecular basis and provide a valuable foundation for further investigation of the roles of DAPs in the process of SE transdifferentiation during cotton totipotency.

Life Cycle Energy Analysis of Reclaimed Water Reuse Projects in Beijing.

To illustrate the benefits of water reuse project, the process-based life cycle analysis (LCA) could be combined with input-output LCA to evaluate the water reuse project. Energy is the only evaluation parameter used in this study. Life cycle assessment of all energy inputs (LCEA) is completed mainly by the life cycle inventory (LCI), taking into account the full life cycle including the construction, the operation, and the demolition phase of the project. Assessment of benefit from water reuse during the life cycle should focus on wastewater discharge reduction and water-saving benefits. The results of LCEA of Beijing water reuse project built in 2014 in a comprehensive way shows that the benefits obtained from the reclaimed water reuse far exceed the life cycle energy consumption. In this paper, the authors apply the LCEA model to estimate the benefits of reclaimed water reuse projects quantitatively.

Study on eco-efficiency of industrial parks in China based on data envelopment analysis.

China's industrial parks have been playing a crucial role on driving regional economy development, but also been posing threats to local environment due to intensive resource consumption and waste emission. Chinese government facilitated eco-industrial development of industrial park, aiming to output more with less environmental burden. In our study, the eco-efficiency levels of 40 Chinese industrial parks in 2012 were assessed and ranked by Data Envelopment Analysis (DEA). This paper applied indicators relevant to resource, economy, and environment from industrial parks which can well reflect the characteristics of eco-efficiency conforming to the concept of sustainability. This paper introduced how to adjust less sustainable parks to be more sustainable according to the DEA results. The roles of industrial added value per capita, industrial structure, environmental policy and development scale as influence factors of eco-efficiency were discussed. The results show that large differences exist in the eco-efficiency of different industrial parks. It is shown that 20% of the parks are relatively efficient. 47% of the study parks being inefficient in terms of scale efficiency show decreasing returns to scale. Policy implementations for the management of industrial parks were also discussed based on the results.

Estimation of GHG Emissions from Water Reclamation Plants in Beijing.

A procedure for estimating Greenhouse gas (GHG) emissions from a wastewater reclamation plant in Beijing was developed based on the process chain model. GHG emissions under two typical water reclamation treatment processes, the coagulation-sedimentation-filtration traditional process and advanced biological treatment process, were examined. The total on-site GHG emissions were estimated to be 0.0056 kg/m3 and 0.6765 kg/m3 respectively, while total off-site GHG emissions were estimated to be 0.3699 kg/m3 and 0.4816 kg/m3. The overall GHG emissions were 0.3755 kg/m3 under the type 1 treatment, which is much lower than that under the type 2 of 1.1581 kg/m3. Emissions from both processes were lower than that from the tap water production. Wastewater reclamation and reuse should be promoted as it not only saves the water resources but also can reduce the GHG emissions. Energy consumption was the most significant source of GHG emissions. Biogas recovery should be employed as it can significantly reduce the GHG emissions, especially under the type 2 treatment process. Considering the wastewater treatment and reclamation process as a whole, the type 2 treatment process has advantages in reducing the GHG emissions per unit of pollutant. This paper provides scientific basis for decision making.

Wastewater reclamation and reuse in China: Opportunities and challenges.

The growing water stress both in terms of water scarcity and quality deterioration promotes the development of reclaimed water as a new water resource use. This paper reviewed wastewater reuse practices in China, and the opportunities and challenges of expanding reclaimed water use were analyzed. Rapid urbanization with the increasing of water demand and wastewater discharge provides an opportunity for wastewater reuse. The vast amount of wastewater discharge and low reclaimed water production mean that wastewater reuse still has a great potential in China. Many environmental and economic benefits and successful reclamation technologies also provide opportunities for wastewater reuse. In addition, the overall strategy in China is also encouraging for wastewater reuse. In the beginning stage of wastewater reclamation and reuse, there are many significant challenges to expand wastewater reuse in China including slow pace in adopting urban wastewater reuse programs, the establishment of integrated water resources management framework and guidelines for wastewater reuse programs, incoherent water quality requirements, the limited commercial development of reclaimed water and the strengthening of public awareness and cooperation among stakeholders.

How many people can the Qinghai-Tibet Plateau hold, and how large cities can be built in recent hundred years?

The Qinghai-Tibet Plateau (QTP) serves as a vital barrier for both national security and ecological preservation. Overpopulation and urban sprawl pose threats to its ecological security, while underpopulation and small urban cities also undermine national security. Hence, optimizing population distribution and urban development on the QTP is crucial for bolstering the national security perimeter and ensuring basic modernisation across China. Nonetheless, understanding the population carrying capacity (CC) of the QTP and how large cities can safeguard both national security and ecological stability remains limited. To address this research gap, we utilised various model algorithms and methodologies to assess the population CC and urban scale of the QTP from seven different perspectives. The results indicate that the permanent population CC of the QTP in 2050 will be 26.2 million people, with an urbanisation level of 57.25 %, thereby allowing 15 million people to enter cities. Thus, the QTP can add 13.07 million people to its permanent population in the future, with a newly added urban population of 8.75 million, increasing the urbanisation level by 9.67 %. The future permanent population will mainly be distributed in the Xining, Lhasa, and Qaidam metropolitan areas. Combined, the permanent and urban populations will account for 38.54 % and 49.84 % of the QTP, respectively. Moreover, these populations will be moderately dispersed in 11 important node cities and more widely dispersed in key border towns. These findings provide a scientific basis for the sustainable development and high-quality urbanisation of the QTP, which have important implications for achieving sustainable development goals, offering crucial references for governments to formulate resource management policies and achieve sustainable resource utilisation.

Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment.

Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.

Environmental stress mediates groundwater microbial community assembly.

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Modulation of thermal stability can enhance the potency of siRNA.

During RNA-induced silencing complex (RISC) assembly the guide (or antisense) strand has to separate from its complementary passenger (or sense) strand to generate the active RISC complex. Although this process was found to be facilitated through sense strand cleavage, there is evidence for an alternate mechanism, in which the strands are dissociated without prior cleavage. Here we show that the potency of siRNA can be improved by modulating the internal thermodynamic stability profile with chemical modifications. Using a model siRNA targeting the firefly luciferase gene with subnanomolar IC50, we found that placement of thermally destabilizing modifications, such as non-canonical bases like 2,4-difluorotoluene or single base pair mismatches in the central region of the sense strand (9-12 nt), significantly improve the potency. For this particular siRNA, the strongest correlation between the decrease in thermal stability and the increase in potency was found at position 10. Controls with stabilized sugar-phosphate backbone indicate that enzymatic cleavage of the sense strand prior to strand dissociation is not required for silencing activity. Similar potency-enhancing effects were observed as this approach was applied to other functional siRNAs targeting a different site on the firefly luciferase transcript or endogenously expressed PTEN.

Dynamic Transcriptome Analysis Reveals Complex Regulatory Pathway Underlying Induction and Dose Effect by Different Exogenous Auxin IAA and 2,4-D During in vitro Embryogenic Redifferentiation in Cotton.

Plant somatic cells can reprogram into differentiated embryos through somatic embryogenesis (SE) on the condition of plant growth regulators (PGRs). RNA sequencing analysis was performed to investigate transcriptional profiling on cotton redifferentiated callus that was induced by different auxin types (IAA and 2,4-D), different concentrations (0, 0.025, and 0.05 mg L-1), and different incubation times (0, 5, and 20 days). Under the 2,4-D induction effect, signal transduction pathways of plant hormones were significantly enriched in the embryogenic response stage (5 days). These results indicated that auxin signal transduction genes were necessary for the initial response of embryogenic differentiation. In the pre-embryonic initial period (20 days), the photosynthetic pathway was significantly enriched. Most differentially expressed genes (DEGs) were downregulated under the induction of 2,4-D. Upon the dose effect of IAA and 2,4-D, respectively, pathways were significantly enriched in phenylpropanoid biosynthesis, fatty acid metabolism, and carbon metabolic pathways. Therefore, primary and secondary metabolism pathways were critical in cotton SE. These results showed that complex synergistic mechanisms involving multiple cellular pathways were the causes of the induction and dose effect of auxin-induced SE. This study reveals a systematic molecular response to auxin signals and reveals the way that regulates embryogenic redifferentiation during cotton SE.