Metabolic Engineering of Corynebacterium glutamicum for the High-Level Production of l-Valine under Aerobic Conditions.

l-Valine, an essential amino acid, serves as a valuable compound in various industries. However, engineering strains with both high yield and purity are yet to be delivered for microbial l-valine production. We engineered a Corynebacterium glutamicum strain capable of highly efficient production of l-valine. We initially introduced an acetohydroxy acid synthase mutant from an industrial l-valine producer and optimized a cofactor-balanced pathway, followed by the activation of the nonphosphoenolpyruvate-dependent carbohydrate phosphotransferase system and the introduction of an exogenous Entner-Doudoroff pathway. Subsequently, we weakened anaplerotic pathways, and attenuated the tricarboxylic acid cycle via start codon substitution in icd, encoding isocitrate dehydrogenase. Finally, to balance bacterial growth and l-valine production, an l-valine biosensor-dependent genetic circuit was established to dynamically repress citrate synthase expression. The engineered strain Val19 produced 103 g/L of l-valine with a high yield of 0.35 g/g glucose and a productivity of 2.67 g/L/h. This represents the highest reported l-valine production in C. glutamicum via direct fermentation and exhibits potential for its industrial-scale production, leveraging the advantages of C. glutamicum over other microbes.

Prediction of systemic inflammatory response syndrome and urosepsis after percutaneous nephrolithotomy by urine culture, stone culture, and renal pelvis urine culture: Systematic review and meta-analysis.

Background: Percutaneous nephrolithotomy (PCNL) is thought to have an increased risk of infectious complications. This study evaluates the predictability of preoperative midstream urine culture (PMUC), stone culture (SC), and renal pelvis urine culture (RPUC) for post-PCNL systemic inflammatory response syndrome (SIRS) or urosepsis. Method: After literature search in electronic databases (Embase, PubMed, Ovid, Science Direct, and Springer), studies were selected by following precise eligibility criteria. The quality of included studies was assessed, and meta-analyses of proportions were performed to seek culture positivity rates and incidence rates of post-PCNL SIRS/urosepsis. Meta-analyses of odds ratios (OR) were performed to evaluate the odds of positivity between SC and PMUC or RPUC, and the odds of post-PCNL SIRS/urosepsis with SC versus PMUC or RPUC. Results: Nineteen studies (4829 patients) were included. Positivity rates of PMUC, SC, and RPUC were 16 % [95 % CI: 12, 20], 21 % [95 % CI: 16, 26] and 10 % [95 % CI: 7, 14] respectively. The odds of positivity were significantly higher for SC compared to PMUC (OR 1.37 [95%CI: 1.02, 1.84]; p = 0.037) or RPUC (OR 1.65 [95%CI: 1.25, 2.18] p < 0.0001). The incidence of post-PCNL SIRS and urosepsis was 21 % [95%CI: 17, 25] and 6 % [95%CI: 3, 10] respectively. The odds of post-PCNL SIRS were significantly higher with SC compared to PMUC (OR 2.45 [95%CI: 1.12, 5.38] p = 0.025) or RPUC (OR 2.10 [95%CI: 1.33, 3.30]; p = 0.001) positivity. The odds of developing urosepsis after PCNL were not significantly different between SC and PMUC positivity (OR 1.874 [95 % CI: 0.943, 3.723]; p = 0.073). Conclusion: The risk of post-PCNL SIRS is found higher with SC than with PMUC or RPUC positivity. However, the risk of urosepsis may not be different between SC and PMUC.

Hydroxylamine-induced activation of permanganate for enhanced oxidation of sulfamethoxazole: Mechanism and products.

Recently, many reagents have been introduced to accelerate the formation of highly reactive intermediate Mn species from permanganate (KMnO4), thereby improving the oxidation activity of KMnO4 towards pollutants. However, most studies have mainly focused on sulfur-containing reducing agents (e.g., bisulfite and sodium sulfite), with little attention paid to nitrogen-containing reducing agents. This study found that hydroxylamine (HA) and hydroxylamine derivatives (HAs) can facilitate KMnO4 in pollutant removal. Taking sulfamethoxazole (SMX) as a target contaminant, the effect of pH, SMX concentration, KMnO4 and HA dosages, and the molar ratio of HA and KMnO4 on the degradation of SMX in the KMnO4/HA process was systematically investigated. Quenching experiments and probe analysis revealed MnO2-catalyzed KMnO4 oxidation, Mn(III) and reactive nitrogen species as the primary active species responsible for SMX oxidation in the KMnO4/HA system. Proposed transformation pathways of SMX in the KMnO4/HA system mainly involve hydroxylation and cleavage reactions. The KMnO4/HA system was more conducive to selective oxidation of SMX, 2,4-dichlorophenol, and several other pollutants, but reluctant to bisphenol S (BPS). Overall, this study proposed an effective system for eliminating pollutants, while providing mechanistic insight into HA-driven KMnO4 activation for environmental remediation.

A Case of Spontaneous Recovery in an Infant with Nail Candidiasis Probably Related to Nail Trauma During Vaginal Delivery.

Onychomycosis in infants is a rare fungal infection. The condition is frequently linked to congenital or secondary immunodeficiency, as well as exposure to contaminated environments. In this report, we present a case of infant onychomycosis, likely infected during birth delivery from the mother with vaginal candidiasis. However, both the infant and the mother recovered spontaneously without any treatment over several months.

Hierarchical lncRNA regulatory network in early-onset severe preeclampsia.

BACKGROUND: Recent studies have shown that several long non-coding RNAs (lncRNAs) in the placenta are associated with preeclampsia (PE). However, the extent to which lncRNAs may contribute to the pathological progression of PE is unclear. RESULTS: Here, we report a hierarchical regulatory network involved in early-onset severe PE (EOSPE). We have carried out transcriptome sequencing on the placentae from patients and normal subjects to identify the differentially expressed genes (DEGs), including some lncRNAs (DElncRNAs). We then constructed a high-quality hierarchical regulatory network of lncRNAs, transcription factors (TFs), and target DEGs, containing 1851 lncRNA-TF interactions and 6901 TF-promoter interactions. The lncRNA-to-target regulatory interactions were further validated by the triplex structures between the DElncRNAs and the promoters of the target DEGs. The DElncRNAs in the regulatory network were clustered into 3 clusters, one containing DElncRNAs correlated with the blood pressure, including FLNB-AS1 with targeting 27.89% (869/3116) DEGs in EOSPE. We further demonstrated that FLNB-AS1 could bind the transcription factor JUNB to regulate a series members of the HIF-1 signaling pathway in trophoblast cells. CONCLUSIONS: Our results suggest that the differential expression of lncRNAs may perturb the lncRNA-TF-DEG hierarchical regulatory network, leading to the dysregulation of many genes involved in EOSPE. Our study provides a new strategy and a valuable resource for studying the mechanism underlying gene dysregulation in EOSPE patients.

PDX1+ cell budding morphogenesis in a stem cell-derived islet spheroid system.

Remarkable advances in protocol development have been achieved to manufacture insulin-secreting islets from human pluripotent stem cells (hPSCs). Distinct from current approaches, we devised a tunable strategy to generate islet spheroids enriched for major islet cell types by incorporating PDX1+ cell budding morphogenesis into staged differentiation. In this process that appears to mimic normal islet morphogenesis, the differentiating islet spheroids organize with endocrine cells that are intermingled or arranged in a core-mantle architecture, accompanied with functional heterogeneity. Through in vitro modelling of human pancreas development, we illustrate the importance of PDX1 and the requirement for EphB3/4 signaling in eliciting cell budding morphogenesis. Using this new approach, we model Mitchell-Riley syndrome with RFX6 knockout hPSCs illustrating unexpected morphogenesis defects in the differentiation towards islet cells. The tunable differentiation system and stem cell-derived islet models described in this work may facilitate addressing fundamental questions in islet biology and probing human pancreas diseases.

A ligand discovery toolbox for the WWE domain family of human E3 ligases.

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15N-NMR-based binding affinity assays and 19F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso-ADP-ribose (iso-ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

Morphological profiling for drug discovery in the era of deep learning.

Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high throughput. These efforts have facilitated understanding of compound mechanism of action, drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.

Optimal conditions and nitrogen removal performance of aerobic denitrifier Comamonas sp. pw-6 and its bioaugmented application in synthetic domestic wastewater treatment.

To assess the possibility of using aerobic denitrification (AD) bacteria with high NO2--N accumulation for nitrogen removal in wastewater treatment, conditional optimization, as well as sole and mixed nitrogen source tests involving AD bacterium, Comamonas sp. pw-6 was performed. The results showed that the optimal carbon source, pH, C/N ratio, rotational speed, and salinity for this strain were determined to be succinate, 7, 20, 160 rpm, and 0%, respectively. Further, this strain preferentially utilized NH4+-N, NO3--N, and NO2--N, and when NO3--N was its sole nitrogen source, 92.28% of the NO3--N (150 mg·L-1) was converted to NO2--N. However, when NH4+-N and NO3--N constituted the mixed nitrogen source, NO3--N utilization by this strain was significantly lower (p < 0.05). Therefore, a strategy was proposed to combine pw-6 bacteria with traditional autotrophic nitrification to achieve the application of pw-6 bacteria in NH4+-N-containing wastewater treatment. Bioaugmented application experiments showed significantly higher NH4+-N removal (5.96 ± 0.94 mg·L-1·h-1) and lower NO3--N accumulation (2.52 ± 0.18 mg·L-1·h-1) rates (p < 0.05) than those observed for the control test. Thus, AD bacteria with high NO2--N accumulation can also be used for practical applications, providing a basis for expanding the selection range of AD strains for wastewater treatment.

UBQLN1 links proteostasis and mitochondria function to telomere maintenance in human embryonic stem cells.

BACKGROUND: Telomeres consist of repetitive DNA sequences at the chromosome ends to protect chromosomal stability, and primarily maintained by telomerase or occasionally by alternative telomere lengthening of telomeres (ALT) through recombination-based mechanisms. Additional mechanisms that may regulate telomere maintenance remain to be explored. Simultaneous measurement of telomere length and transcriptome in the same human embryonic stem cell (hESC) revealed that mRNA expression levels of UBQLN1 exhibit linear relationship with telomere length. METHODS: In this study, we first generated UBQLN1-deficient hESCs and compared with the wild-type (WT) hESCs the telomere length and molecular change at RNA and protein level by RNA-seq and proteomics. Then we identified the potential interacting proteins with UBQLN1 using immunoprecipitation-mass spectrometry (IP-MS). Furthermore, the potential mechanisms underlying the shortened telomeres in UBQLN1-deficient hESCs were analyzed. RESULTS: We show that Ubiquilin1 (UBQLN1) is critical for telomere maintenance in human embryonic stem cells (hESCs) via promoting mitochondrial function. UBQLN1 deficiency leads to oxidative stress, loss of proteostasis, mitochondria dysfunction, DNA damage, and telomere attrition. Reducing oxidative damage and promoting mitochondria function by culture under hypoxia condition or supplementation with N-acetylcysteine partly attenuate the telomere attrition induced by UBQLN1 deficiency. Moreover, UBQLN1 deficiency/telomere shortening downregulates genes for neuro-ectoderm lineage differentiation. CONCLUSIONS: Altogether, UBQLN1 functions to scavenge ubiquitinated proteins, preventing their overloading mitochondria and elevated mitophagy. UBQLN1 maintains mitochondria and telomeres by regulating proteostasis and plays critical role in neuro-ectoderm differentiation.

Electrochemical Enantioselective C-H Annulation by Achiral Rhodium(III)/Chiral Brønsted Base Domino Catalysis.

Rhodium(III)-catalyzed enantioselective C-H activation has emerged as a powerful tool for assembling enabling chiral molecules. However, this approach is significantly hampered by the cumbersome synthetic routes for preparing chiral rhodium catalysts. In sharp contrast, we herein report on an electrochemical domino catalysis system that exploits an achiral Cp*-rhodium catalyst along with an easily accessible chiral Brønsted base for an enantioselective C-H activation/annulation reaction of alkenes by benzoic acids. Our strategy offers an environmentally benign and most user-friendly approach for assembling synthetically useful chiral phthalides in good enantioselectivity, employing electricity as the sustainable oxidant.

Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice.

Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.

A computational neural model that incorporates both intrinsic dynamics and sensory feedback in the Aplysia feeding network.

Studying the nervous system underlying animal motor control can shed light on how animals can adapt flexibly to a changing environment. We focus on the neural basis of feeding control in Aplysia californica. Using the Synthetic Nervous System framework, we developed a model of Aplysia feeding neural circuitry that balances neurophysiological plausibility and computational complexity. The circuitry includes neurons, synapses, and feedback pathways identified in existing literature. We organized the neurons into three layers and five subnetworks according to their functional roles. Simulation results demonstrate that the circuitry model can capture the intrinsic dynamics at neuronal and network levels. When combined with a simplified peripheral biomechanical model, it is sufficient to mediate three animal-like feeding behaviors (biting, swallowing, and rejection). The kinematic, dynamic, and neural responses of the model also share similar features with animal data. These results emphasize the functional roles of sensory feedback during feeding.

Metatranscriptome and small RNA sequencing revealed a mixed infection of newly identified bymovirus and bean yellow mosaic virus on peas.

Peas (Pisum sativum L.) are widely cultivated in temperate regions and are susceptible hosts for various viruses across different families. The discovery and identification of new viruses in peas has significant implications for field disease management. Here, we identified a mixed infection of two viruses from field-collected peas exhibiting virus-like symptoms using metatranscriptome and small RNA sequencing techniques. Upon identification, one of the viruses was determined to be a newly isolated and discovered bymovirus from peas, named "pea bymovirus 1 (PBV1)". The other was identified as a novel variant of bean yellow mosaic virus (BYMV-HZ1). Subsequently, mechanical inoculation and RT-PCR assays confirmed that both viruses could be inoculated back onto peas and tobaccos, showing mixed infection by PBV1 and BYMV-HZ1. To our knowledge, this is the first isolation of a bymovirus from pea and the first documented case of mixed infection of peas by PBV1 and BYMV-HZ1 in China.

Fluidized Reduction Kinetics of Boron-Bearing Iron Concentrate by Hydrogen at Low Temperatures Based on Model-Fitting and Model-Free Methods.

Pyrometallurgy is the most effective way to comprehensively utilize boron-bearing iron concentrate, and there is an urgency for an environmentally friendly and efficient method to achieve the prereduction of boron-bearing iron concentrate. In this study, the mechanism and kinetics of isothermal hydrogen reduction of boron-bearing iron concentrate in a fluidized bed at 500-570 °C were discussed. The reduction degree was quantified in combination with the online gas composition analysis technique, and the phase and microstructure of the reduced products were characterized. The results exhibited that the apparent activation energy remained constant during the whole reduction process, with average values of 50.67 and 48.08 kJ/mol calculated by the model-free and model-fitting methods, respectively, and the reaction was controlled by the contracting sphere model. The formation of a microporous metallic iron facilitated the rapid penetration of hydrogen to the reaction interface. Therefore, the intrinsic chemical reaction at the interface determined the whole reaction process.

Analysis and Visualization of Single-Cell Sequencing Data with Scanpy and MetaCell: A Tutorial.

The emergence and development of single-cell RNA sequencing (scRNA-seq) techniques enable researchers to perform large-scale analysis of the transcriptomic profiling at cell-specific resolution. Unsupervised clustering of scRNA-seq data is central for most studies, which is essential to identify novel cell types and their gene expression logics. Although an increasing number of algorithms and tools are available for scRNA-seq analysis, a practical guide for users to navigate the landscape remains underrepresented. This chapter presents an overview of the scRNA-seq data analysis pipeline, quality control, batch effect correction, data standardization, cell clustering and visualization, cluster correlation analysis, and marker gene identification. Taking the two broadly used analysis packages, i.e., Scanpy and MetaCell, as examples, we provide a hands-on guideline and comparison regarding the best practices for the above essential analysis steps and data visualization. Additionally, we compare both packages and algorithms using a scRNA-seq dataset of the ctenophore Mnemiopsis leidyi, which is representative of one of the earliest animal lineages, critical to understanding the origin and evolution of animal novelties. This pipeline can also be helpful for analyses of other taxa, especially prebilaterian animals, where these tools are under development (e.g., placozoan and Porifera).

Identifying acute illness phenotypes via deep temporal interpolation and clustering network on physiologic signatures.

Using clustering analysis for early vital signs, unique patient phenotypes with distinct pathophysiological signatures and clinical outcomes may be revealed and support early clinical decision-making. Phenotyping using early vital signs has proven challenging, as vital signs are typically sampled sporadically. We proposed a novel, deep temporal interpolation and clustering network to simultaneously extract latent representations from irregularly sampled vital signs and derive phenotypes. Four distinct clusters were identified. Phenotype A (18%) had the greatest prevalence of comorbid disease with increased prevalence of prolonged respiratory insufficiency, acute kidney injury, sepsis, and long-term (3-year) mortality. Phenotypes B (33%) and C (31%) had a diffuse pattern of mild organ dysfunction. Phenotype B's favorable short-term clinical outcomes were tempered by the second highest rate of long-term mortality. Phenotype C had favorable clinical outcomes. Phenotype D (17%) exhibited early and persistent hypotension, high incidence of early surgery, and substantial biomarker incidence of inflammation. Despite early and severe illness, phenotype D had the second lowest long-term mortality. After comparing the sequential organ failure assessment scores, the clustering results did not simply provide a recapitulation of previous acuity assessments. This tool may impact triage decisions and have significant implications for clinical decision-support under time constraints and uncertainty.

Freeze-thaw aged polyethylene and polypropylene microplastics alter enzyme activity and microbial community composition in soil.

In cold regions, microplastics (MPs) in the soil undergo freeze-thaw (FT) aging process. Little is known about how FT aged MPs influence soil physico-chemical properties and microbial communities. Here, two environmentally relevant concentrations (50 and 500 mg/kg) of 50 and 500 µm polyethylene (PE) and polypropylene (PP) MPs treated soils were subjected to 45-day FT cycles (FTCs). Results showed that MPs experienced surface morphology, hydrophobicity and crystallinity alterations after FTCs. After 45-day FTCs, the soil urease (SUE) activity in control (MPs-free group that underwent FTCs) was 33.49 U/g. SUE activity in 50 µm PE group was reduced by 19.66 %, while increased by 21.16 % and 37.73 % in 500 µm PE and PP groups compared to control. The highest Shannon index was found in 50 µm PP-MPs group at 50 mg/kg, 2.26 % higher than control (7.09). Compared to control (average weighted degree=8.024), all aged MPs increased the complexity of network (0.19-1.43 %). Bacterial biomarkers of aged PP-MPs were associated with pollutant degradation. Aged PP-MPs affected genetic information, cellular processes, and disrupted the biosynthesis of metabolites. This study provides new insights into the potential hazards of MPs after FTCs on soil ecosystem in cold regions.