Scalable, compressed phenotypic screening using pooled perturbations.

High-throughput phenotypic screens using biochemical perturbations and high-content readouts are constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to reduce required sample size, labor and cost. We demonstrate the increased efficiency of compressed experimental designs compared to conventional approaches through benchmarking with a bioactive small-molecule library and a high-content imaging readout. We then apply compressed screening in two biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to a library of recombinant tumor microenvironment protein ligands, uncovering reproducible phenotypic shifts induced by specific ligands distinct from canonical reference signatures and correlated with clinical outcome. In the second, we identify the pleotropic modulatory effects of a chemical compound library with known mechanisms of action on primary human peripheral blood mononuclear cell immune responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts and basic biological inquiry.

Single-pixel phase imaging via a complex-valued Zernike basis.

Single-pixel phase imaging (SPPI) utilizes a single-pixel detector combined with interferometry to capture phase information of an unknown field. However, to reconstruct an M × N image, normally M × N modulations and detections are required, leading to a long imaging time for SPPI. Here, a complex-valued Zernike basis SPPI (Zernike-SPPI) is proposed to achieve phase reconstruction at as high quality as possible with a very low sampling ratio. Simulations and experiments demonstrate that Zernike-SPPI achieves better imaging quality at a sampling ratio of less than 10% compared to the state-of-the-art SPPI techniques based on Hadamard basis. This means Zernike-SPPI can obtain a high-quality phase image with less imaging time. This work offers a solution to achieve fast SPPI while guaranteeing quality phase reconstruction as high as possible.

Remediation of cadmium contaminated soil using electrokinetic-phytoremediation system with rotary switching electrodes.

Considering both electrokinetic remediation and phytoremediation have limitations, an electrokinetic phytoremediation (EP) system was constructed to obtain efficient and environmentally friendly remediation results. This study indicates that the electric field can promote the absorption of Cd by ryegrass with little impact on soil physicochemical properties under the condition of rotary switching electrodes, and the accumulation of Cd in the aboveground and underground parts of ryegrass increased by 145.2% and 93.7%, respectively. The DC electric field combined with ryegrass under rotary switching electrode mode proved to be the optimal condition for the remediation of Cd contaminated soil with a remediation efficiency of 66.7%. Moreover, the rotary switching of the electrodes alleviated the suppression of the growth of ryegrass by the DC electric field. During the EP remediation process, the electric field promoted the transformation of the residue state of Cd to the other forms, which accelerated the desorption rate of Cd from the soil and facilitated the migration of Cd into plants. In conclusion, EP is a green and efficient remediation technology for heavy metal contaminated soil with good application prospects.

Efficient reduction of CO2 and inhibition of hydrogen precipitation by polyoxometalate photocatalyst modified with the metal Mn.

Photocatalytic reduction of CO2 to chemical fuels is attractive for solving both the greenhouse effect and the energy crisis, but the key challenge is to design and synthesize photocatalysts with remarkable performance under visible light irradiation. Efficient catalytic carbon dioxide reduction (CO2RR) with light is considered a promising sustainable and clean approach to solve environmental problems. Herein, we found a new photocatalyst ([Mn(en)2]6[V12B18O54(OH)6]) (abbreviated as Mn6V12) based on the modifiability of polyoxometalates, in which Mn acts as a modifying unit to efficiently reduce CO2 to CO and effectively inhibit the hydrogen precipitation reaction. This Mn modified polyoxometalate catalyst has a maximum CO generation rate of 4625.0 µmol g-1 h-1 and a maximum H2 generation rate of 499.6 µmol g-1 h-1, with a selectivity of 90.3% for CO generation and 9.7% for H2 generation. This polyoxometalate photocatalyst can effectively reduce CO and inhibit the hydrogen precipitation reaction. It provides a new idea for the efficient photocatalytic carbon dioxide reduction (CO2RR) with polyoxometalate catalysts.

Controllable Construction of a Mo2C/MoO2 Interface with an Ideal Mo2C/MoO2 Ratio for Efficient Electrocatalytic Nitrogen Reduction to Ammonia.

Electrocatalytic nitrogen reduction reaction (NRR) is considered to be a viable contender for the production of NH3. However, due to the sluggish adsorption and activation of the electrocatalyst toward inert N2 molecules, there is an urgent need for developing effective catalysts to facilitate the reaction. Inspired by natural nitrogenase, in which Mo atoms are the active centers, Mo-based electrocatalysts have received considerable attention, but further exploration is still necessary. Interface-engineered electrocatalysts can effectively optimize the absorption and activation of the catalytic active center for N2 and thus improve the electrocatalytic activity of NRR. However, the lack of studies for controllably constructing an optimal ratio of two phases at the interface hinders the development of NRR electrocatalysts. Herein, a series of Mo2C/MoO2 interface-engineered electrocatalysts with various Mo2C/MoO2 ratios were constructed by controlling the Y dosages. The controlled experimental results verified that the catalytic activity of NRR, the dosage of Y, and the ratio of Mo2C/MoO2 were strongly correlated. Density functional theory calculations show that the C-Mo-O coordination at the Mo2C/MoO2 interface can optimize the reaction path and reduce the energy barrier of the reaction intermediates, thereby enhancing the reaction kinetics of NRR.

High-Resolution Estimates of N2O Emissions from Inland Waters and Wetlands in China.

Inland waters (rivers, lakes, and reservoirs) and wetlands (marshes and coastal wetlands) represent large and continuous sources of nitrous oxide (N2O) emissions, in view of adequate biomass and anaerobic conditions. Considerable uncertainties remain in quantifying spatially explicit N2O emissions from aquatic systems, attributable to the limitations of models and a lack of comprehensive data sets. Herein, we conducted a synthesis of 1659 observations of N2O emission rates to determine the major environmental drivers across five aquatic systems. A framework for spatially explicit estimates of N2O emissions in China was established, employing a data-driven approach that upscaled from site-specific N2O fluxes to robust multiple-regression models. Results revealed the effectiveness of models incorporating soil organic carbon and water content for marshes and coastal wetlands, as well as water nitrate concentration and dissolved organic carbon for lakes, rivers, and reservoirs for predicting emissions. Total national N2O emissions from inland waters and wetlands were 1.02 × 105 t N2O yr-1, with contributions from marshes (36.33%), rivers (27.77%), lakes (25.27%), reservoirs (6.47%), and coastal wetlands (4.16%). Spatially, larger emissions occurred in the Songliao River Basin and Continental River Basin, primarily due to their substantial terrestrial biomass. This study offers a vital national inventory of N2O emissions from inland waters and wetlands in China, providing paradigms for the inventorying work in other countries and insights to formulate effective mitigation strategies for climate change.

Non-destructive strategy to extract sustainable helix and high-strength Musa core fibers for rapid water conduction and evaporation.

The reuse and development of natural waste resources is a hotspots and challenges in the research of new fiber materials and the resolution of environmental concern globally. Herein, this study aimed to develop a simple and direct manual extraction process to extract Musa core fibers (MCFs) for rapid water conduction and evaporation. Through simple processes such as ring cutting and stretching, this green and non-destructive inside-out extraction strategy enabled Musa fibers to be naturally and harmlessly degummed from natural Musa stems, with good maintenance of the fiber structure and highly helical morphology. The extracted fibers are composed of regularly and closely arranged cellulose nanofibrils in the shape of ribbon spirally arranged multi-filaments, and the single filament is about 2.65 µm. The high-purity fibers exhibit ultra-high tensile strength under a non-destructive extraction process, and the ultimate tensile strength in dry state is as high as 742.95 MPa. The tensile strength is affected by the number of fiber bundles, which shows that tensile strength and tensile modulus is higher than those of vascular bundle fibers in dry or wet condition. In addition, the MCFs membrane indicates good water conductivity, with a water absorption height of 50 mm for the sample in only 60 s. Moreover, the water evaporation rate of MCFs reaches 1.37 kg m-2 h-1 in 30 min, which shows that MCFs have excellent water conductivity and evaporation rate compared with ordinary cotton fibers. These results indicate that MCFs have great potential in replacing the use of chemical methods to extract fibers from vascular bundles, providing an effective way to achieve sustainability in quick-drying applications, as well as in the sustainable development of natural waste resources.

Surface wettability control and electron transport regulation in zerovalent iron for enhanced removal of emerging polystyrene microplastics-heavy metal contaminants.

Emerging microplastics-heavy metal (MPs-HM) contaminants in wastewaters pose an emerging health and environmental risk due to their persistence and increasing ecological risks (e.g., "Trojan horse" effect). Hence, removing MPs in solution and preventing secondary releases of HM has become a key challenge when tackling with MPs pollution. Leveraging the hydrophobic nature of MPs and the electron transfer efficiency from Fe0 to HM, we demonstrate an alkylated and sulfidated nanoscale zerovalent iron (AS-nZVI) featuring a delicate "core-shell-hydrophobic film" nanostructure. Exemplified by polystyrene (PS) MPs-Pb(II) removal, the three nanocomponents offer synergistic functions for the rapid separation of MPs, as well as the reduction and stabilization of Pb(II). The outmost hydrophobic film of AS-nZVI greatly improves the anticorrosion performance of nanoscale zerovalent iron and the enrichment abilities of hydrophobic MPs, achieving a maximum removal capacity of MPs to 2725.87 mgMPs·gFe-1. This MPs enrichment promotes the subsequent reductive removal of Pb(II) through the electron transfer from the iron core of AS-nZVI to Pb(II), a process further strengthened by the introduced sulfur. When considering the inevitable aging of MPs in wastewaters due to mechanical wear or microbial degradation, our study concurrently examines the efficiencies and behaviors of AS-nZVI in removing virgin-MPs-Pb(II) and aged-MPs-Pb(II). The batch results reveal that AS-nZVI has an exceptional ability to remove above 99.6 % Pb(II) for all reaction systems. Overall, this work marks a pioneering effort in highlighting the importance of MPs-toxin combinations in dealing with MPs contamination and in demonstrating the utility of nZVI techniques for MPs-contaminated water purification.

Correlation Study on the Prognostic Value of miR-21 and S-100B Protein Levels in Neonatal Hypoxic-Ischemic Encephalopathy Undergoing Hypothermia Therapy.

OBJECTIVE: To evaluate the variations in serum levels of microRNA-21 (miR-21) and S-100B protein in neonates with hypoxic-ischemic encephalopathy (HIE) after receiving hypothermia therapy and explore the correlation of these biomarkers with the neurodevelopmental prognosis of the infants. METHODS: This retrospective analysis included 90 neonatal HIE patients diagnosed and treated between January 2019 and December 2022. Real-time quantitative PCR and enzyme-linked immunosorbent assay (ELISA) methods were used to measure miR-21 and S-100B protein levels. Neurodevelopmental assessments were conducted at one year, and follow-up was performed using the Bayley Scales of Infant and Toddler Development third edition. Statistical analysis was carried out using SPSS software, with t-tests for continuous variables, chi-square tests for categorical data, Pearson correlation coefficient for correlation analysis, and multivariate regression analysis to adjust for confounding factors. RESULTS: After hypothermia therapy, the observation group showed a significant decrease in miR-21 and S-100B protein levels (P < 0.001), and neurodevelopmental scores were significantly higher than the control group (P < 0.05). Correlation analysis indicated a negative correlation between miR-21 and neurodevelopmental scores (r=-0.62, P < 0.001), as well as a negative correlation between S-100B protein levels (r=-0.76, P < 0.001). Multivariate regression analysis demonstrated that miR-21 levels and S-100B protein levels maintained independent negative correlations with neurodevelopmental scores (P < 0.001). CONCLUSION: Hypothermia therapy significantly reduces serum levels of miR-21 and S-100B protein in neonatal HIE patients and may be associated with better prognosis. miR-21 and S-100B serve as prognostic biomarkers, aiding in predicting and improving the treatment outcomes and long-term prognosis of neonatal HIE.

Sulfidated nanoscale zero valent iron for in situ immobilization of hexavalent chromium in soil and response of indigenous microbes.

This study aimed to investigate the immobilization efficiency of sulfidated nanoscale zero valent iron on Cr(VI) in soil. Reactions between sulfidated nanoscale zero valent iron and Cr(VI) in soil system and effects of sulfidated nanoscale zero valent iron on microbes had been demonstrated. Solid characterization results confirmed the incorporation of sulfur into nanoscale zero valent iron. Furthermore, the main oxidation products of iron after the reactions were magnetite, goethite and lepidocrocite. Fe-Cr complexes indicated that Cr(VI) was reduced to Cr(III). The results of 16 S rRNA gene analysis indicated that the sulfidated nanoscale zero valent iron had a limited bactericidal effect but further stimulated the sulfite reductase gene population, representing its positive effect for the soil remediation. The study showed that some microflora such as Protobacteria were promoted, while others community such as Firmicutes, were depressed. Furthermore, Cr mainly converted from a high toxic state such as exchangeable (EX) to less bioavailable state such as iron-manganese oxides bound (OX) and organic matter-bound (OM), thus reducing the toxicity of Cr when sulfidated nanoscale zero valent iron was added. High immobilization efficiency of the Cr(VI) compared to nanoscale zero valent iron indicated an improvement on selectivity and reactivity after sulfidation. Overall, sulfidated nanoscale zero valent iron was promising for the immobilization of Cr(VI) immobilization soil.

Subchronic exposure to di-(2-ethylhexyl) phthalate (DEHP) elicits blood-brain barrier dysfunction and neuroinflammation in male C57BL/6J mice.

BACKGROUND: Exposure to di-(2-ethylhexyl) phthalate (DEHP) can cause neurotoxicity but the mechanism is not clear. Blood brain barrier (BBB) is one of the most important tissues to protect the brain. However, whether DEHP can disrupt the BBB or not remains unclear. The objective of this study is to investigate the potential effects of subchronic DEHP exposure on BBB integrity and discuss the role of BBB in DEHP inducible neurotoxicity with an emphasis on neuroinflammatory responses. Male adult C57BL/6J mice were orally administered with vehicle or 200 or 750 mg/kg/day DEHP for 90 days. Subchronic exposure to high-dose DEHP increased water intake but decreased body weight and brain weight. The concentrations of DEHP metabolites increased in serum from all DEHP-exposed groups while increased in brain only from the high-dose group. DEHP induced neurobehavioural alterations and damaged hippocampal neurons. DEHP increased BBB permeability by Evans blue (EB) extravasation and decreased tight junction proteins (ZO-1, occludin, and claudin-5) while presenting a neuroinflammatory feature characterized by the upregulated inflammatory mediators TNF-α and the NLRP3/caspase-1/IL-1ß inflammasome pathway. Our data provide new insights into neurotoxicity caused by subchronic DEHP exposure, which is probably involved in BBB dysfunction and neuroinflammatory responses.

xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes.

To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are geared toward a complete reconstruction for all families in an entire clade. Here we describe an update to the xenoGI software package which allows users to perform such an analysis using the newly developed DTLOR (duplication-transfer-loss-origin-rearrangement) reconciliation model starting from genome sequences as input.

Compressed phenotypic screens for complex multicellular models and high-content assays.

High-throughput phenotypic screens leveraging biochemical perturbations, high-content readouts, and complex multicellular models could advance therapeutic discovery yet remain constrained by limitations of scale. To address this, we establish a method for compressing screens by pooling perturbations followed by computational deconvolution. Conducting controlled benchmarks with a highly bioactive small molecule library and a high-content imaging readout, we demonstrate increased efficiency for compressed experimental designs compared to conventional approaches. To prove generalizability, we apply compressed screening to examine transcriptional responses of patient-derived pancreatic cancer organoids to a library of tumor-microenvironment (TME)-nominated recombinant protein ligands. Using single-cell RNA-seq as a readout, we uncover reproducible phenotypic shifts induced by ligands that correlate with clinical features in larger datasets and are distinct from reference signatures available in public databases. In sum, our approach enables phenotypic screens that interrogate complex multicellular models with rich phenotypic readouts to advance translatable drug discovery as well as basic biology.

Microbes team with nanoscale zero-valent iron: A robust route for degradation of recalcitrant pollutants.

Integrating nanoscale zero-valent iron (nZVI) with biological treatment processes holds the promise of inheriting significant advantages from both environmental nano- and bio-technologies. nZVI and microbes can perform in coalition in direct contact and act simultaneously, or be maintained in separate reactors and operated sequentially. Both modes can generate enhanced performance for wastewater treatment and environmental remediation. nZVI scavenges and eliminates toxic metals, and enhances biodegradability of some recalcitrant contaminants while bioprocesses serve to mineralize organic compounds and further remove impurities from wastewater. This has been demonstrated in a number of recent works that nZVI can substantially augment the performance of conventional biological treatment for wastewaters from textile and nonferrous metal industries. Our recent laboratory and field tests show that COD of the industrial effluents can be reduced to a record-low of 50 ppm. Recent literature on the theory and applications of the nZVI-bio system is highlighted in this mini review.

A win-win solution to chromate removal by sulfidated nanoscale zero-valent iron in sludge.

This study investigates the reaction between sulfidated nanoscale zero valent iron (S-nZVI) and Cr(VI) in the sludge system and explores the effect of S-nZVI on microbes. Results of the batch experiments indicated that the optimal Cr(VI) removal capacity (35.3 mg/g) was reached when the S/Fe ratio was at 0.05. It was about 20-time higher than that of nanoscale zero valent iron (nZVI) (<2.0 mg/g). However, the removal efficiency decreased as the S/Fe molar ratio further increased. Solid characterizations revealed that the S-nZVI consisted of a Fe0 core encapsulated by a flake FeS shell and had a similar "core-shell" structure to that of the nZVI. X-ray photoelectron spectroscopy (XPS) indicated that Cr(VI) was reduced to less toxic Cr(III). In addition, the 16 S rRNA gene and cryo-scanning electron microscopy (cryo-SEM) results showed S-nZVI mildly influenced the initial microbial diversity. Some microflora including Caldiserica, Planctomycetes were promoted, while others groups such as Actinobacteria, Bacteroidetes and Chloroflexi were inhibited: specifically, bacteria such as Proteobacteria (possibly related to sulfide oxidization) began to develop after the S-nZVI feeding. The high Cr(VI) removal efficiency and the mildly influenced microbial diversity make the usage of S-nZVI a win-win solution for Cr(VI) removal in sludge.

Chronic inflammation as a potential mediator between phthalate exposure and depressive symptoms.

BACKGROUND: A few studies have reported phthalate exposure as a risk factor for depressive symptoms, but the results have been inconsistent. Whether chronic inflammation mediates the relationship between phthalates (PAEs) and depressive symptoms remains unclear. In this study, we establish mediating models of inflammatory factors and explore the mediating role of chronic inflammation in the association between PAEs exposure and depressive symptoms. METHODS: The sample included 989 participants from the Study on Health and Environment of the Elderly in Lu'an City, Anhui Province. Geriatric depression scale (GDS-30) was used to screen depressive symptoms of the elderly. The levels of seven kinds of PAEs in urine samples and four inflammatory factors in serum of the elderly were measured. To establish the mediating effect of inflammatory factors to explore the potential effect of PAEs exposure on the increased odds of depressive symptoms. RESULTS: Adjusted for multiple variables, the highest tertiles of Mono (2-ethylhexyl) phthalate (MEHP) (95%CI = 1.051-2.112), Mono benzyl phthalate (MBzP) (95%CI = 1.016-2.082) and Mono butyl phthalate (MBP) (95%CI = 1.102-2.262) were positively correlated with depressive symptoms. The mediating effect of IL-6 and generalized inflammation factor between MEHP exposure and depressive symptoms were 15.96% (95%CI=0.0288-0.1971) and 14.25% (95%CI = 0.0167-0.1899). CONCLUSIONS: High levels of MEHP, MBzP and MBP increased the odds of depressive symptoms in the elderly, and chronic inflammation had a partial mediating effect on the increased odds of depressive symptoms due to MEHP exposure.

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.

Maximum parsimony reconciliation in the DTLOR model.

BACKGROUND: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. RESULTS: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. CONCLUSIONS: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.

Comparative Proteomic Characterization of Ventral Hippocampus in Susceptible and Resilient Rats Subjected to Chronic Unpredictable Stress.

Chronic stress is an essential factor leading to depression. However, there exist individual differences in people exposed to the same stressful stimuli. Some people display negative psychology and behavior, while others are normal. Given the importance of individual difference, finding differentially expressed proteins in stress-resistant and stress-susceptible groups has great significance for the study of pathogenesis and treatment of depression. In this study, stress-susceptible rats and stress-resilient rats were first distinguished by sucrose preference test. These stress-susceptible rats also displayed depression-like behaviors in forced swimming test and open field test. Then, we employed label-free quantitative proteomics to analyze proteins in the ventral hippocampus. There were 4,848 proteins totally identified. Based on statistical analysis, we found 276 differentially expressed proteins. Bioinformatics analysis revealed that the biological processes of these differential proteins were related to mitochondrion organization, protein localization, coenzyme metabolic process, cerebral cortex tangential migration, vesicle-mediated transport, and so on. The KEGG pathways were mainly involved in metabolic pathways, axon guidance, autophagy, and tight junction. Furthermore, we ultimately found 20 stress-susceptible proteins and two stress-resilient proteins. These stress-related proteins could not only be potential biomarkers for depression diagnosis but also contribute to finding new therapeutic targets and providing personalized medicine.