Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome.

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

Development of an enzyme-linked immunosorbent assay using a monoclonal antibody to a dominant epitope in non-structural protein 4 of porcine reproductive and respiratory syndrome virus.

Porcine reproductive and respiratory syndrome (PRRS) caused by the PRRS virus (PRRSV) is one of the most severe swine diseases causing great economic losses for the international swine industry. Non-structural protein 4 (NSP4) is critical to the life cycle of PRRSV and contains dominant B cell epitopes. This study prepared a monoclonal antibody against Nsp4, and 2D11, which contained the sequence 138KQGGGIVTRPSGQFCN153, was confirmed as the epitope. A 2D11-based double antibody sandwich enzyme-linked immunosorbent assay (dasELISA) was next developed with a cut value of 0.1987. A total of 1354 pig serum samples were detected by dasELISA and compared to a commercial ELISA kit (N-coated iELISA), resulting in a positive coincidence rate of 98.8% and negative coincidence rate of 96.9%. A total of 119 sera were positive by dasELISA while negative by iELISA. Higher positive rates by dasELISA were found in pig farms where PRRSV antibody levels varied widely. These results indicated that the dasELISA was a useful tool to detect PRRSV antibody in clinical samples.

Rational design of diblock copolymer enables efficient cytosolic protein delivery.

Polymer-mediated cytosolic protein delivery demonstrates a promising strategy for the development of protein therapeutics. Here, we propose a new designed diblock copolymer which realizes efficient cytosolic protein delivery both in vitro and in vivo. The polymer contains one protein-binding block composed of phenylboronic acid (PBA) and N-(3-dimethylaminopropyl) (DMAP) pendant units for protein binding and endosomal escape, respectively, followed by the response to ATP enriched in the cytosol which triggers the protein release. The other block is PEG designed to improve particle size control and circulation in vivo. By optimizing the block composition, sequence and length of the copolymer, the optimal one (BP20) was identified with the binding block containing 20 units of both PBA and DMAP, randomly distributed along the chain. When mixed with proteins, the BP20 forms stable nanoparticles and mediates efficient cytosolic delivery of a wide range of proteins including enzymes, toxic proteins and CRISPR/Cas9 ribonucleoproteins (RNP), to various cell lines. The PEG block, especially when further modified with folic acid (FA), enables tumor-targeted delivery of Saporin in vivo, which significantly suppresses the tumor growth. Our results shall inspire the design of novel polymeric vehicles with robust capability for cytosolic protein delivery, which holds great potential for both biological research and therapeutic applications.

A Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance of a Parkinsonism/Spinocerebellar-Ataxia Complex.

This study aimed to identify possible pathogenic genes in a 90-member family with a rare combination of multiple neurodegenerative disease phenotypes, which has not been depicted by the known neurodegenerative disease. We performed physical and neurological examinations with International Rating Scales to assess signs of ataxia, Parkinsonism, and cognitive function, as well as brain magnetic resonance imaging scans with seven sequences. We searched for co-segregations of abnormal repeat-expansion loci, pathogenic variants in known spinocerebellar ataxia-related genes, and novel rare mutations via whole-genome sequencing and linkage analysis. A rare co-segregating missense mutation in the CARS gene was validated by Sanger sequencing and the aminoacylation activity of mutant CARS was measured by spectrophotometric assay. This pedigree presented novel late-onset core characteristics including cerebellar ataxia, Parkinsonism, and pyramidal signs in all nine affected members. Brain magnetic resonance imaging showed cerebellar/pons atrophy, pontine-midline linear hyperintensity, decreased rCBF in the bilateral basal ganglia and cerebellar dentate nucleus, and hypo-intensities of the cerebellar dentate nuclei, basal ganglia, mesencephalic red nuclei, and substantia nigra, all of which suggested neurodegeneration. Whole-genome sequencing identified a novel pathogenic heterozygous mutation (E795V) in the CARS gene, meanwhile, exhibited none of the known repeat-expansions or point mutations in pathogenic genes. Remarkably, this CARS mutation causes a 20% decrease in aminoacylation activity to charge tRNACys with L-cysteine in protein synthesis compared with that of the wild type. All family members carrying a heterozygous mutation CARS (E795V) had the same clinical manifestations and neuropathological changes of Parkinsonism and spinocerebellar-ataxia. These findings identify novel pathogenesis of Parkinsonism-spinocerebellar ataxia and provide insights into its genetic architecture.

Integrating proximal soil sensing data and environmental variables to enhance the prediction accuracy for soil salinity and sodicity in a region of Xinjiang Province, China.

Soil salinization and sodification, the primary causes of land degradation and desertification in arid and semi-arid regions, demand effective monitoring for sustainable land management. This study explores the utility of partial least square (PLS) latent variables (LVs) derived from visible and near-infrared (Vis-NIR) spectroscopy, combined with remote sensing (RS) and auxiliary variables, to predict electrical conductivity (EC) and sodium absorption ratio (SAR) in northern Xinjiang, China. Using 90 soil samples from the Karamay district, machine learning models (Random Forest, Support Vector Regression, Cubist) were tested in four scenarios. Modeling results showed that RS and Land use alone were unreliable predictors, but the addition of topographic attributes significantly improved the prediction accuracy for both EC and SAR. The incorporation of PLS LVs derived from Vis-NIR spectroscopy led to the highest performance by the Random Forest model for EC (CCC = 0.83, R2 = 0.80, nRMSE = 0.48, RPD = 2.12) and SAR (CCC = 0.78, R2 = 0.74, nRMSE = 0.58, RPD = 2.25). The variable importance analysis identified PLS LVs, certain topographic attributes (e.g., valley depth, elevation, channel network base level, diffuse insolation), and specific RS data (i.e., polarization index of VV + VH) as the most influential predictors in the study area. This study affirms the efficiency of Vis-NIR data for digital soil mapping, offering a cost-effective solution. In conclusion, the integration of proximal soil sensing techniques and highly relevant topographic attributes with the RF model has the potential to yield a reliable spatial model for mapping soil EC and SAR. This integrated approach allows for the delineation of hazardous zones, which in turn enables the consideration of best management practices and contributes to the reduction of the risk of degradation in salt-affected and sodicity-affected soils.

Structural insights into somatostatin receptor 5 bound with cyclic peptides.

Somatostatin receptor 5 (SSTR5) is highly expressed in ACTH-secreting pituitary adenomas and is an important drug target for the treatment of Cushing's disease. Two cyclic SST analog peptides (pasireotide and octreotide) both can activate SSTR5 and SSTR2. Pasireotide is preferential binding to SSTR5 than octreotide, while octreotide is biased to SSTR2 than SSTR5. The lack of selectivity of both pasireotide and octreotide causes side effects, such as hyperglycemia, gastrointestinal disturbance, and abnormal glucose homeostasis. However, little is known about the binding and selectivity mechanisms of pasireotide and octreotide with SSTR5, limiting the development of subtype-selective SST analog drugs specifically targeting SSTR5. Here, we report two cryo-electron microscopy (cryo-EM) structures of SSTR5-Gi complexes activated by pasireotide and octreoitde at resolutions of 3.09 Å and 3.24 Å, respectively. In combination with structural analysis and functional experiments, our results reveal the molecular mechanisms of ligand recognition and receptor activation. We also demonstrate that pasireotide preferentially binds to SSTR5 through the interactions between Tyr(Bzl)/DTrp of pasireotide and SSTR5. Moreover, we find that the Q2.63, N6.55, F7.35 and ECL2 of SSTR2 play a crucial role in octreotide biased binding of SSTR2. Our results will provide structural insights and offer new opportunities for the drug discovery of better selective pharmaceuticals targeting specific SSTR subtypes.

D-mannose alleviates intervertebral disc degeneration through glutamine metabolism.

BACKGROUND: Intervertebral disc degeneration (IVDD) is a multifaceted condition characterized by heterogeneity, wherein the balance between catabolism and anabolism in the extracellular matrix of nucleus pulposus (NP) cells plays a central role. Presently, the available treatments primarily focus on relieving symptoms associated with IVDD without offering an effective cure targeting its underlying pathophysiological processes. D-mannose (referred to as mannose) has demonstrated anti-catabolic properties in various diseases. Nevertheless, its therapeutic potential in IVDD has yet to be explored. METHODS: The study began with optimizing the mannose concentration for restoring NP cells. Transcriptomic analyses were employed to identify the mediators influenced by mannose, with the thioredoxin-interacting protein (Txnip) gene showing the most significant differences. Subsequently, small interfering RNA (siRNA) technology was used to demonstrate that Txnip is the key gene through which mannose exerts its effects. Techniques such as colocalization analysis, molecular docking, and overexpression assays further confirmed the direct regulatory relationship between mannose and TXNIP. To elucidate the mechanism of action of mannose, metabolomics techniques were employed to pinpoint glutamine as a core metabolite affected by mannose. Next, various methods, including integrated omics data and the Gene Expression Omnibus (GEO) database, were used to validate the one-way pathway through which TXNIP regulates glutamine. Finally, the therapeutic effect of mannose on IVDD was validated, elucidating the mechanistic role of TXNIP in glutamine metabolism in both intradiscal and orally treated rats. RESULTS: In both in vivo and in vitro experiments, it was discovered that mannose has potent efficacy in alleviating IVDD by inhibiting catabolism. From a mechanistic standpoint, it was shown that mannose exerts its anti-catabolic effects by directly targeting the transcription factor max-like protein X-interacting protein (MondoA), resulting in the upregulation of TXNIP. This upregulation, in turn, inhibits glutamine metabolism, ultimately accomplishing its anti-catabolic effects by suppressing the mitogen-activated protein kinase (MAPK) pathway. More importantly, in vivo experiments have further demonstrated that compared with intradiscal injections, oral administration of mannose at safe concentrations can achieve effective therapeutic outcomes. CONCLUSIONS: In summary, through integrated multiomics analysis, including both in vivo and in vitro experiments, this study demonstrated that mannose primarily exerts its anti-catabolic effects on IVDD through the TXNIP-glutamine axis. These findings provide strong evidence supporting the potential of the use of mannose in clinical applications for alleviating IVDD. Compared to existing clinically invasive or pain-relieving therapies for IVDD, the oral administration of mannose has characteristics that are more advantageous for clinical IVDD treatment.

Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species.

BACKGROUD: The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS: The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION: The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

An innovative exploration to identify and isolate the dominant-flocculated-species from polytitanium chloride synthesized by electrodialysis.

Abundance of dominant-flocculated-species is the key to determine coagulation performance of coagulant. Titanium-based coagulants have garnered considerable attention due to their high coagulation efficiency, but with a current challenge of the identification and isolation of the dominant-flocculated-species. Herein, polytitanium chloride (PTC), enriched with dominant-flocculated-species, was successfully synthesized by electrodialysis through accurate micro-interface control of the reaction among Ti-hydrolyzed-species and OH-. Special attention was paid to a feasible and high-effective strategy to isolate the dominant-flocculated-species from PTC through one-step rapid ultrafiltration. Selective preference was the ultrafiltration membranes (made of polyethersulfone) with a molecular weight cut-off of 5 kDa, which enabled the isolation of the dominant-flocculated-species, named PTC-5k. Results from the electrospray time-of-flight mass spectrometry (ESI-TOF-MS) proved a large proportion of the small and medium-sized hydrolyzed products as dominant-flocculated-species in PTC-5k, with the main signals concentrated between m/z 100 and 500. This composition achieved approximately 15.0% higher removal of organic matter with a 33.0% reduction in dosage compared to PTC. Unique snowflake-like branched structure of PTC-5k enhanced the coagulation mechanisms of sweeping and adsorption-bridging flocculation. Worth noting was the more compact flocs formed by PTC-5k than PTC, which was the probable reason for the mitigated fouling of ceramic membrane when PTC-5k was utilized as pre-treatment methodology. Continuous operation of ceramic membrane filtration up to 30 h, demonstrated 30% improvement in stable flux compared to PTC. This study provides the strategy for the isolation of Ti-dominant-flocculated-species, and lays the foundation for practical application.

Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil.

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.

Spiral Large-Dimension Microfluidic Channel for Flow-Rate- and Particle-Size-Insensitive Focusing by the Stabilization and Acceleration of Secondary Flow.

Inertial microfluidics has demonstrated its ability to focus particles in a passive and straightforward manner. However, achieving flow-rate- and particle-size-insensitive focusing in large-dimension channels with a simple design remains challenging. In this study, we developed a spiral microfluidic with a large-dimension channel to achieve inertial focusing. By designing a unique "big buffering area" and a "small buffering area" in the spiral microchannel, we observed the stabilization and acceleration of secondary flow. Our optimized design allowed for efficient (>99.9%) focusing of 15 µm particles within a wide range of flow rates (0.5-4.5 mL/min) during a long operation duration (0-60 min). Additionally, we achieved effective (>95%) focusing of different-sized particles (7, 10, 15, and 30 µm) and three types of tumor cells (K562, HeLa, and MCF-7) near the inner wall of the 1 mm wide outlet when applying different flow rates (1-3 mL/min). Finally, successful 3D cell focusing was achieved within an optimized device, with the cells positioned at a distance of 50 µm from the wall. Our strategy of stabilizing and accelerating Dean-like secondary flow through the unique configuration of a "big buffering area" and a "small buffering area" proved to be highly effective in achieving inertial focusing that is insensitive to the flow rate and particle size, particularly in large-dimension channels. Consequently, it shows great potential for use in hand-operated microfluidic tools for flow cytometry.

Co-fermentation of titanium-flocculated-sludge with food waste towards simultaneous water purification and resource recovery.

Recovery of resources from domestic sewage and food waste has always been an international-thorny problem. Titanium-based flocculation can achieve high-efficient destabilization, quick concentration and separation of organic matter from sewage to sludge. This study proposed co-fermentation of the titanium-flocculated sludge (Ti-loaded sludge) and food waste towards resource recovery by converting organic matter to value-added volatile fatty acids (VFAs) and inorganic matter to struvite and TiO2 nanoparticles. When Ti-loaded sludge and food waste were co-fermented at a mass ratio of 3:1, the VFAs yield reached 3725.2 mg-COD/L (VFAs/SCOD 91.0%), which was more than 4 times higher than the case of the sludge alone. The 48-day semicontinuous co-fermentation demonstrated stable long-term operation, yielding VFAs at 2529.0 mg-COD/L (VFAs/SCOD 89.8%) and achieving a high CODVFAs/NNH4 of 58.9. Food waste provided sufficient organic substrate, enriching plenty of acid-producing fermentation bacteria (such as Prevotella 7 about 21.0% and Bacteroides about 9.4%). Moreover, metagenomic sequencing analysis evidenced the significant increase of the relative gene abundance corresponding to enzymes in pathways, such as extracellular hydrolysis, substrates metabolism, and VFAs biosynthesis. After fermentation, the precious element P (≥ 99.0%) and extra-added element Ti (≥99.0%) retained in fermented residues, without releasing to VFAs supernatant, which facilitated the direct re-use of VFAs as resource. Through simple and commonly used calcination and acid leaching methodologies, 80.9% of element P and 82.1% of element Ti could be successfully recovered as struvite and TiO2 nanoparticles, respectively. This research provides a strategy for the co-utilization of domestic sludge and food waste, which can realize both reduction of sludge and recovery of resources.

Dynamic Transformation of Nano-MoS2 in a Soil-Plant System Empowers Its Multifunctionality on Soybean Growth.

Molybdenum disulfide (nano-MoS2) nanomaterials have shown great potential for biomedical and catalytic applications due to their unique enzyme-mimicking properties. However, their potential agricultural applications have been largely unexplored. A key factor prior to the application of nano-MoS2 in agriculture is understanding its behavior in a complex soil-plant system, particularly in terms of its transformation. Here, we investigate the distribution and transformation of two types of nano-MoS2 (MoS2 nanoparticles and MoS2 nanosheets) in a soil-soybean system through a combination of synchrotron radiation-based X-ray absorption near-edge spectroscopy (XANES) and single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS). We found that MoS2 nanoparticles (NPs) transform dynamically in soil and plant tissues, releasing molybdenum (Mo) and sulfur (S) that can be incorporated gradually into the key enzymes involved in nitrogen metabolism and the antioxidant system, while the rest remain intact and act as nanozymes. Notably, there is 247.9 mg/kg of organic Mo in the nodule, while there is only 49.9 mg/kg of MoS2 NPs. This study demonstrates that it is the transformation that leads to the multifunctionality of MoS2, which can improve the biological nitrogen fixation (BNF) and growth. Therefore, MoS2 NPs enable a 30% increase in yield compared to the traditional molybdenum fertilizer (Na2MoO4). Excessive transformation of MoS2 nanosheets (NS) leads to the overaccumulation of Mo and sulfate in the plant, which damages the nodule function and yield. The study highlights the importance of understanding the transformation of nanomaterials for agricultural applications in future studies.

Effects of nitrogen supply on hydrogen-oxidizing bacterial enrichment to produce microbial protein: Comparing nitrogen fixation and ammonium assimilation.

To investigate the effects of nitrogen source supply on microbial protein (MP) production by hydrogen-oxidizing bacteria (HOB) under continuous feed gas provision, a sequencing batch culture comparison (N2 fixation versus ammonium assimilation) was performed. The results confirmed that even under basic cultivation conditions, N2-fixing HOB (NF-HOB) communities showed higher levels of CO2 and N2 fixation (190.45 mg/L Δ CODt and 11.75 mg/L Δ TNbiomass) than previously known, with the highest biomass yield being 0.153 g CDW/g COD-H2. Rich ammonium stimulated MP synthesis and the biomass accumulation of communities (increased by 7.4 ～ 14.3 times), presumably through the enhancement of H2 and CO2 absorption. The micro mechanism may involve encouraging the enrichment of species like Xanthobacter and Acinetobacter then raising the abundance of nitrogenase and glutamate synthase to facilitate the nitrogen assimilation. This would provide NF-HOB with ideas for optimizing their MP synthesis activity.

CircLARP1B promotes pyroptosis of high glucose-induced renal mesangial cells by regulating the miR-578/TLR4 axis.

BACKGROUND: Diabetic nephropathy (DN) is a main cause of end-stage renal disease with high mortality. Circular RNAs (circRNAs) are associated with the pathogenesis of DN. This study aimed to explore the role of circLARP1B in DN. METHODS: The levels of circLARP1B, miR-578, TLR4 in DN and high glucose (HG)-treated cells using quantitative real-time PCR. Their relationship was analyzed using dual-luciferase reporter assay. The biological behaviors were assessed by MTT assay, EDU assay, flow cytometry, ELISA, and western blot. RESULTS: The results indicated that circLARP1B and TLR4 were highly expressed, and miR-578 was low expressed in patients with DN and HG-induced cells. Knockdown of circLARP1B promoted the proliferation and cell cycle, and inhibited pyroptosis and inflammation of HG-induced cells. CircLARP1B is a sponge of miR-578, which targets TLR4. Rescue experiments showed that inhibition of miR-578 reversed the effects of circLARP1B knockdown, while TLR4 reversed the effects of miR-578. CONCLUSION: CircLARP1B/miR-578/TLR4 axis suppressed the proliferation, blocked cell cycle at the G0-G1 phase, promoted pyroptosis, and inflammatory factor release of renal mesangial cells induced by HG. The findings suggested that circLARP1B may be a target for the treatment of DN.

Deep learning models for preoperative T-stage assessment in rectal cancer using MRI: exploring the impact of rectal filling.

Background: The objective of this study was twofold: firstly, to develop a convolutional neural network (CNN) for automatic segmentation of rectal cancer (RC) lesions, and secondly, to construct classification models to differentiate between different T-stages of RC. Additionally, it was attempted to investigate the potential benefits of rectal filling in improving the performance of deep learning (DL) models. Methods: A retrospective study was conducted, including 317 consecutive patients with RC who underwent MRI scans. The datasets were randomly divided into a training set (n = 265) and a test set (n = 52). Initially, an automatic segmentation model based on T2-weighted imaging (T2WI) was constructed using nn-UNet. The performance of the model was evaluated using the dice similarity coefficient (DSC), the 95th percentile Hausdorff distance (HD95), and the average surface distance (ASD). Subsequently, three types of DL-models were constructed: Model 1 trained on the total training dataset, Model 2 trained on the rectal-filling dataset, and Model 3 trained on the non-filling dataset. The diagnostic values were evaluated and compared using receiver operating characteristic (ROC) curve analysis, confusion matrix, net reclassification index (NRI), and decision curve analysis (DCA). Results: The automatic segmentation showed excellent performance. The rectal-filling dataset exhibited superior results in terms of DSC and ASD (p = 0.006 and 0.017). The DL-models demonstrated significantly superior classification performance to the subjective evaluation in predicting T-stages for all test datasets (all p < 0.05). Among the models, Model 1 showcased the highest overall performance, with an area under the curve (AUC) of 0.958 and an accuracy of 0.962 in the filling test dataset. Conclusion: This study highlighted the utility of DL-based automatic segmentation and classification models for preoperative T-stage assessment of RC on T2WI, particularly in the rectal-filling dataset. Compared with subjective evaluation, the models exhibited superior performance, suggesting their noticeable potential for enhancing clinical diagnosis and treatment practices.

High-Throughput Blood Plasma Extraction in a Dimension-Confined Double-Spiral Channel.

Microfluidic technologies enabling the control of secondary flow are essential for the successful separation of blood cells, a process that is beneficial for a wide range of medical research and clinical diagnostics. Herein, we introduce a dimension-confined microfluidic device featuring a double-spiral channel designed to regulate secondary flows, thereby enabling high-throughput isolation of blood for plasma extraction. By integrating a sequence of micro-obstacles within the double-spiral microchannels, the stable and enhanced Dean-like secondary flow across each loop can be generated. This setup consequently prompts particles of varying diameters (3, 7, 10, and 15 µm) to form different focusing states. Crucially, this system is capable of effectively separating blood cells of different sizes with a cell throughput of (2.63-3.36) × 108 cells/min. The concentration of blood cells in outlet 2 increased 3-fold, from 1.46 × 108 to 4.37 × 108, while the number of cells, including platelets, exported from outlets 1 and 3 decreased by a factor of 608. The engineering approach manipulating secondary flow for plasma extraction points to simplicity in fabrication, ease of operation, insensitivity to cell size, high throughput, and separation efficiency, which has potential utility in propelling the development of miniaturized diagnostic devices in the field of biomedical science.

Utilization of halophytes in saline agriculture and restoration of contaminated salinized soils from genes to ecosystem: Suaeda salsa as an example.

Halophytes can be used to screen genes for breeding salt-tolerant crops and are of great value in the restoration of salinized or contaminated soils. However, the potential of halophytes in improving saline soils remains limited. In this paper, based on the latest research progress, we use Suaeda salsa L. as an example to evaluate the value of halophytes in developing saline agriculture including: 1) some defined salt-resistance genes and high-affinity nitrate transporter genes in the species for breeding salt-tolerance and nitrogen efficiency crops; 2) the value of S. salsa and microorganisms from S. salsa in remediation of heavy metal contaminated and organic polluted saline soils; and 3) the capacity to remove salts from soils and the application of the species. In conclusion, S. salsa has high value as a candidate to explore the theoretical base and practical application for utilizing halophytes to improve salinized soils from genes to ecosystem.

Flow-Rate-Insensitive Plasma Extraction by the Stabilization and Acceleration of Secondary Flow in the Ultralow Aspect Ratio Spiral Channel.

Although microfluidic devices have made remarkable strides in blood cell separation, there is still a need for further development and improvement in this area. Herein, we present a novel ultralow aspect ratio (H/W = 1:36) spiral channel microfluidic device with ordered micro-obstacles for sheathless and flow-rate-insensitive blood cell separation. By introducing ordered micro-obstacles into the spiral microchannels, reduced magnitude fluctuations in secondary flow across different loops can be obtained through geometric confinement. As a result, the unique Dean-like secondary flow can effectively enhance the separation efficiency of particles in different sizes ranging from 3 to 15 µm. Compared to most existing microfluidic devices, our system offers several advantages of easy manufacturing, convenient operation, long-term stability, highly efficient performance (up to 99.70% rejection efficiency, including platelets), and most importantly, insensitivity to cell sizes as well as flow rates (allowing for efficient separation of different-sized blood cells in a wide flow rate from 1.00 to 2.50 mL/min). The unique characteristics, such as ultralow aspect ratio, sequential micro-obstacles, and controlled secondary flow, make our device a promising solution for practical plasma extraction in biomedical research and clinical applications.