Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.

Accelerated discovery of CO2 electrocatalysts using active machine learning.

The rapid increase in global energy demand and the need to replace carbon dioxide (CO2)-emitting fossil fuels with renewable sources have driven interest in chemical storage of intermittent solar and wind energy1,2. Particularly attractive is the electrochemical reduction of CO2 to chemical feedstocks, which uses both CO2 and renewable energy3-8. Copper has been the predominant electrocatalyst for this reaction when aiming for more valuable multi-carbon products9-16, and process improvements have been particularly notable when targeting ethylene. However, the energy efficiency and productivity (current density) achieved so far still fall below the values required to produce ethylene at cost-competitive prices. Here we describe Cu-Al electrocatalysts, identified using density functional theory calculations in combination with active machine learning, that efficiently reduce CO2 to ethylene with the highest Faradaic efficiency reported so far. This Faradaic efficiency of over 80 per cent (compared to about 66 per cent for pure Cu) is achieved at a current density of 400 milliamperes per square centimetre (at 1.5 volts versus a reversible hydrogen electrode) and a cathodic-side (half-cell) ethylene power conversion efficiency of 55 ± 2 per cent at 150 milliamperes per square centimetre. We perform computational studies that suggest that the Cu-Al alloys provide multiple sites and surface orientations with near-optimal CO binding for both efficient and selective CO2 reduction17. Furthermore, in situ X-ray absorption measurements reveal that Cu and Al enable a favourable Cu coordination environment that enhances C-C dimerization. These findings illustrate the value of computation and machine learning in guiding the experimental exploration of multi-metallic systems that go beyond the limitations of conventional single-metal electrocatalysts.

Improved pathogenicity prediction for rare human missense variants.

The success of personalized genomic medicine depends on our ability to assess the pathogenicity of rare human variants, including the important class of missense variation. There are many challenges in training accurate computational systems, e.g., in finding the balance between quantity, quality, and bias in the variant sets used as training examples and avoiding predictive features that can accentuate the effects of bias. Here, we describe VARITY, which judiciously exploits a larger reservoir of training examples with uncertain accuracy and representativity. To limit circularity and bias, VARITY excludes features informed by variant annotation and protein identity. To provide a rationale for each prediction, we quantified the contribution of features and feature combinations to the pathogenicity inference of each variant. VARITY outperformed all previous computational methods evaluated, identifying at least 10% more pathogenic variants at thresholds achieving high (90% precision) stringency.

Shifting landscapes of human MTHFR missense-variant effects.

Most rare clinical missense variants cannot currently be classified as pathogenic or benign. Deficiency in human 5,10-methylenetetrahydrofolate reductase (MTHFR), the most common inherited disorder of folate metabolism, is caused primarily by rare missense variants. Further complicating variant interpretation, variant impacts often depend on environment. An important example of this phenomenon is the MTHFR variant p.Ala222Val (c.665C>T), which is carried by half of all humans and has a phenotypic impact that depends on dietary folate. Here we describe the results of 98,336 variant functional-impact assays, covering nearly all possible MTHFR amino acid substitutions in four folinate environments, each in the presence and absence of p.Ala222Val. The resulting atlas of MTHFR variant effects reveals many complex dependencies on both folinate and p.Ala222Val. MTHFR atlas scores can distinguish pathogenic from benign variants and, among individuals with severe MTHFR deficiency, correlate with age of disease onset. Providing a powerful tool for understanding structure-function relationships, the atlas suggests a role for a disordered loop in retaining cofactor at the active site and identifies variants that enable escape of inhibition by S-adenosylmethionine. Thus, a model based on eight MTHFR variant effect maps illustrates how shifting landscapes of environment- and genetic-background-dependent missense variation can inform our clinical, structural, and functional understanding of MTHFR deficiency.

Understanding the Poly (Triazine Imide) Crystals Formation Process: The Conversion from Heptazine to Triazine.

Poly (triazine imide) (PTI) generally obtained via ionothermal synthesis features extended π-conjugation and enhanced crystallinity. However, in-depth investigation of the polycondensation process for PTI is an onerous task due to multiple influencing factors and limited characterization techniques. Herein, to simplify the polymerization route and exclude non-essential factors, PTI was prepared by calcining only melamine and LiCl. This study aims to identify the pivotal role of LiCl in PTI formation, which can convert heptazine-based intermediates into more stable triazine-based PTI framework. Based on this discovery, we demonstrate the transformation process of the prepared samples from amorphous Bulk g-C3 N4 to regular PTI, and further prove that the reaction with LiCl causes disruption of heptazine covalent organic frameworks. Additionally, the PTI exhibits higher photocatalytic water splitting performance due to efficient charge carrier mobility and separation, as well as faster reaction kinetics. This discovery deepens understanding of the polycondensation process of PTI crystals and provides insights toward the rational design of crystalline carbon nitride-based semiconductors.

Synchrotron Radiation Based X-ray Absorption Spectroscopy: Fundamentals and Applications in Photocatalysis.

Photocatalysis is one of the most promising green technologies to utilize solar energy for clean energy achievement and environmental governance. There is a knotty problem to rational designing high-performance photocatalyst, which largely depends on an in-depth insight into their structure-activity relationships and complex photocatalytic reaction mechanisms. Synchrotron radiation based X-ray absorption spectroscopy (XAS) is an important characterization method for photocatlayst to offer the element-specific key geometric and electronic structural information at the atomic level, on this basis, time-resolved XAS technique has a huge impact on mechanistic understanding of photochemical reaction owing to their powerful ability to probe, in real-time, the electronic and geometric structures evolution within photocatalysis reactions. This review will focus on the fundamentals of XAS and their applications in photocatalysis. The detailed applications obtained from XAS is described through the following aspects: 1) identifying local structure of photocatalyst; 2) uncovering in situ structure and chemical state evolution during photocatalysis; 3) revealing the photoexcited process. We will provide an in depth understanding on how the XAS method can guide the rational design of highly efficient photocatalyst. Finally, a systematic summary of XAS and related significance is made and the research perspectives are suggested.

Facet-Dependent Photocatalytic Behavior of Rutile TiO2 for the Degradation of Volatile Organic Compounds: In Situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy and Density Functional Theory Investigations.

In this study, a custom rutile titanium dioxide (TiO2) photocatalyst with a single exposed surface was utilized to investigate the facet-dependent photocatalytic mechanism of toluene. The degradation of toluene was dynamically monitored using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) technology coupled with theoretical calculations. The findings demonstrated that the photocatalytic degradation rate on the TiO2 (001) surface was nearly double that observed on the TiO2 (110) surface. This remarkable enhancement can be attributed to the heightened stability in the adsorption of toluene molecules and the concurrent reduction in the energy requirement for the ring-opening process of benzoic acid on the TiO2 (001) surface. Moreover, the TiO2 (001) surface generated a greater number of reactive oxygen species (ROS), thereby promoting the separation of photogenerated charge carriers and concurrently diminishing their recombination rates, amplifying the efficiency of photocatalysis. This research provides an innovative perspective for a more comprehensive understanding of the photocatalytic degradation mechanism of TiO2 and presents promising prospects for significant applications in environmental purification and energy fields.

Photo-thermal Catalytic Hydrogenation of Halogenated Nitrobenzenes over Ni/P25 Catalyst.

As haloanilines (HANs) are important organic intermediates and fine chemicals, their preparation over non-noble-metal-based catalysts by catalytic hydrogenation has attracted wide attention. However, the reaction suffers from relatively harsh conditions. Herein, we found that a 3.5%Ni/P25 catalyst exhibited superior photo-thermal catalytic activity with a TOFs of 5207 h-1 for hydrogenation of p-chloronitrobenzene (p-CNB) to p-chloroaniline under a 300 W full spectrum, which was much higher than that of photo- and thermal catalysis alone. Moreover, the 3.5%Ni/P25 catalyst could be recycled 4 times and was effective for the hydrogenation of various halonitrobenzenes (HNBs) with superior selectivity. Furthermore, the kinetic research showed that the excellent catalytic performance could be attributed to the better activation and dissociation of H2 by photo-thermal catalysis and the hydrogenation of p-CNB obeyed the condensation routine by ionic hydrogenation over 3.5%Ni/P25.

Anomalous Nernst Effect Induced Terahertz Emission in a Single Ferromagnetic Film.

Despite its important role in understanding ultrafast spin dynamics and revealing novel spin/orbit effects, the mechanism of the terahertz (THz) emission from a single ferromagnetic nanofilm upon a femtosecond laser pump still remains elusive. Recent experiments have shown exotic symmetry, which is not expected from the routinely adopted mechanism of ultrafast demagnetization. Here, by developing a bidirectional pump-THz emission spectroscopy and associated symmetry analysis method, we set a benchmark for the experimental distinction of the THz emission induced by various mechanisms. Our results unambiguously unveil a new mechanism─anomalous Nernst effect (ANE) induced THz emission due to the ultrafast temperature gradient created by a femtosecond laser. Quantitative analysis shows that the THz emission exhibits interesting thickness dependence where different mechanisms dominate at different thickness ranges. Our work not only clarifies the origin of the ferromagnetic-based THz emission but also offers a fertile platform for investigating the ultrafast optomagnetism and THz spintronics.

Insights into symbiotic interactions from metatranscriptome analysis of deep-sea mussel Gigantidas platifrons under long-term laboratory maintenance.

Symbioses between invertebrates and chemosynthetic bacteria are of fundamental importance in deep-sea ecosystems, but the mechanisms that enable their symbiont associations are still largely undescribed, owing to the culturable difficulties of deep-sea lives. Bathymodiolinae mussels are remarkable in their ability to overcome decompression and can be maintained successfully for an extended period under atmospheric pressure, thus providing a model for investigating the molecular basis of symbiotic interactions. Herein, we conducted metatranscriptome sequencing and gene co-expression network analysis of Gigantidas platifrons under laboratory maintenance with gradual loss of symbionts. The results revealed that one-day short-term maintenance triggered global transcriptional perturbation in symbionts, but little gene expression changes in mussel hosts, which were mainly involved in responses to environmental changes. Long-term maintenance with depleted symbionts induced a metabolic shift in the mussel host. The most notable changes were the suppression of sterol biosynthesis and the complementary activation of terpenoid backbone synthesis in response to the reduction of bacteria-derived terpenoid sources. In addition, we detected the upregulation of host proteasomes responsible for amino acid deprivation caused by symbiont depletion. Additionally, a significant correlation between host microtubule motor activity and symbiont abundance was revealed, suggesting the possible function of microtubule-based intracellular trafficking in the nutritional interaction of symbiosis. Overall, by analyzing the dynamic transcriptomic changes during the loss of symbionts, our study highlights the nutritional importance of symbionts in supplementing terpenoid compounds and essential amino acids and provides insight into the molecular mechanisms and strategies underlying the symbiotic interactions in deep-sea ecosystems.

Construction of TiO2 /SrTiO3 Heterojunction Derived from Monolayer Ti3 C2 MXene for Efficient Photocatalytic Overall Water Splitting.

Construction of heterojunction at the atomic scale to ensure efficient charge separation for improvement of photocatalytic water splitting is challenging. Herein, a facile hydrothermal method has been applied for the in situ fabrication of TiO2 /SrTiO3 heterojunction, using the monolayer Ti3 C2 MXene as the template and reactant. It is found that the sample with the hydrothermal reaction time of 60 min exhibits the highest H2 evolution rate with the sacrificial reagent, due to the efficient charge separation of TiO2 /SrTiO3 heterojunction as Ti3 C2 derivative. In addition, the sample shows the best overall water splitting performance at a hydrothermal reaction time of 120 min, where TiO2 is nearly converted to SrTiO3 , due to the fast kinetic process and low structural defects of SrTiO3 . This work not only provides a simple strategy for the fabrication of heterojunction photocatalysts but also demonstrates the difference in optimization of half-reaction and overall water splitting reaction.

Photocatalytic Z-scheme Overall Water Splitting: Insight into Different Optimization Strategies for Powder Suspension and Particulate Sheet Systems.

Achieving solar light-driven photocatalytic overall water splitting is the ideal and ultimate goal for solving energy and environment issues. Photocatalytic Z-scheme overall water splitting has undergone considerable development in recent years; specific approaches include a powder suspension Z-scheme system with a redox shuttle and a particulate sheet Z-scheme system. Of these, a particulate sheet has achieved a benchmark solar-to-hydrogen efficiency exceeding 1.1 %. Nevertheless, owing to intrinsic differences in the components, structure, operating environment, and charge transfer mechanism, there are several differences between the optimization strategies for a powder suspension and particulate sheet Z-scheme. Unlike a powder suspension Z-scheme with a redox shuttle, the particulate sheet Z-scheme system is more like a miniaturized and parallel p/n photoelectrochemical cell. In this review, we summarize the optimization strategies for a powder suspension Z-scheme with a redox shuttle and particulate sheet Z-scheme. In particular, attention has been focused on choosing appropriate redox shuttle and electron mediator, facilitating the redox shuttle cycle, avoiding redox mediator-induced side reactions, and constructing a particulate sheet. Challenges and prospects in the development of efficient Z-scheme overall water splitting are also briefly discussed.

In Situ Growth Facilitating the Piezo-Photocatalytic Effect of Zn1-xCdxS/ZnO Nanorods for Highly Efficient H2 Production.

Photocatalytic H2 production holds promise for alleviating energy and environmental issues. The separation of photoinduced charge carriers plays vital roles in enhancing the activity of photocatalytic H2 production. The piezoelectric effect has been proposed to be effective in facilitating the separation of charge carriers. However, the piezoelectric effect is usually restricted by the noncompact contact between the polarized materials and semiconductors. In this study, Zn1-xCdxS/ZnO nanorod arrays on stainless steel for piezo-photocatalytic H2 production are fabricated by an in situ growth method, achieving an electronic-level contact between Zn1-xCdxS and ZnO. The separation and migration of photogenerated charge carriers in Zn1-xCdxS are significantly improved by the piezoelectric effect induced by ZnO under mechanical vibration. Consequently, under solar and ultrasonic irradiation, the H2 production rate of Zn1-xCdxS/ZnO nanorod arrays achieves 20.96 µmol h-1 cm-2, which is 4 times higher than that under solar irradiation. Such a performance can be attributed to the synergies of the piezoelectric field of bent ZnO nanorods and the built-in electric field of the Zn1-xCdxS/ZnO heterostructure, which efficiently separate the photoinduced charge carriers. This study provides a new strategy to couple polarized materials and semiconductors for highly efficient piezo-photocatalytic H2 production.

Long-term outcomes after enterostomy for very early-onset inflammatory bowel disease with interleukin-10 signaling deficiency.

BACKGROUND: Very early-onset inflammatory bowel disease (VEOIBD) with interleukin-10 (IL10R) signaling deficiency usually requires enterostomy in patients who are refractory to traditional treatment. This study aimed to evaluate long-term outcomes after enterostomy for VEOIBD patients with IL10R signaling deficiency. METHODS: The medical records of all patients undergoing enterostomy for signaling deficiency were retrospectively assessed during 2012.1-2022.7 in a tertiary teaching hospital, Children's Hospital of Fudan University, Shanghai, China. Data on disease history, diagnosis and details of enterostomy and stoma closure and follow-up were collected. Univariate and multivariate logistic regression analyses were used to evaluate the risk factors associated with the long-term outcome of delayed stoma closure. RESULTS: A total of 46 patients underwent an enterostomy, 19 who required emergency enterostomy and 27 with selective enterostomy. After ten years of follow-up, 35 patients underwent hematopoietic stem cell transplantation (HSCT), and 25 patients were alive after HSCT. The median timeframe between HSCT and stoma closure was 19.6 [15.9,26.2] months. Nineteen patients underwent stoma closure and had an average age of 3.9 ± 1.5 years; 6 patients were waiting for stoma closure. Based on a univariate logistic model, risk factors significantly associated with late stoma closure were age at enterostomy and age at HSCT. However, multivariate logistic regression showed no statistically significant factor associated with late stoma closure. There was no significant difference between the stoma closure group and delay closure group in the z scores of weight for age at follow up. CONCLUSIONS: This study determined the long-term outcomes after enterostomy for VEOIBD with interleukin-10 signaling deficiency. The appropriate time point of enterostomy and HSCT may improve quality of life in the long term.

First case report of pustules associated with Escherichia fergusonii in the chinese pangolin (Manis pentadactyla aurita).

BACKGROUND: Escherichia fergusonii is a common conditionally pathogenic bacterium that infects humans and animals. E. fergusonii has been reported to cause diarrhea, respiratory disease, and septicemia, but it is rarely reported to cause skin infections in animals. E. fergusonii has been isolated from the skin and muscular tissue of Chinese pangolin (Manis pentadactyla aurita). To date, there have been no reports of Chinese pangolins with clinical signs of skin diseases. CASE PRESENTATION: This case report describes the clinical case of a subadult (bodyweight: 1.1 kg) female Chinese pangolin from wild rescue with pustules and subcutaneous suppurative infection due to E. fergusonii in the abdominal skin. Bacterial culture, Biochemical analysis, PCR and histopathology were utilized to identify the bacteria in the pustule puncture fluid and infected tissue. To the best of our knowledge, this is the first report of E. fergusonii-related pustules on a Chinese pangolin. CONCLUSION: This case report presents the first observed skin infection in a Chinese pangolin. E. fergusonii infection should be considered as a possible differential diagnosis of pustules and subcutaneous suppurative skin conditions in Chinese pangolins, and we also provide several recommendations for the diagnosis and treatment of this disease.

[Effect of Juanbi Qianggu Formula on biological behaviors of fibroblast-like synoviocytes in rheumatoid arthritis by regulating FGFR1 signaling pathway based on network pharmacology and cell function experiments].

This study aimed to explore the molecular mechanism of Juanbi Qianggu Formula(JBQGF), an empirical formula formulated by the prestigious doctor in traditional Chinese medicine, in the treatment of rheumatoid arthritis based on network pharmacology and cell function experiments. The main active components and targets of JBQGF were obtained through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) and Encyclopedia of Traditional Chinese Medicine(ETCM), and the core targets underwent functional enrichment analysis and signaling pathway analysis. Cytoscape 3.6.0 was used to construct a visualized "active component-target-signaling pathway" network of JBQGF. After screening, nine potential pathways of JBQGF were obtained, mainly including G protein-coupled receptor signaling pathway and tyrosine kinase receptor signaling pathway. As previously indicated, the fibroblast growth factor receptor 1(FGFR1) signaling pathway was highly activated in active fibroblast-like synoviocytes(FLS) in rheumatoid arthritis, and cell and animal experiments demonstrated that inhibition of the FGFR1 signaling pathway could significantly reduce joint inflammation and joint destruction in collagen-induced arthritis(CIA) rats. In terms of the tyrosine kinase receptor signal transduction pathway, the analysis of its target genes revealed that FGFR1 might be a potential target of JBQGF for rheumatoid arthritis treatment. The biological effect of JBQGF by inhibiting FGFR1 phosphorylation was preliminarily verified by Western blot, Transwell invasion assay, and pannus erosion assay, thereby inhibiting matrix metalloproteinase 2(MMP2) and receptor activator of nuclear factor-κB ligand(RANKL) and suppressing the invasion of fibroblasts in rheumatoid arthritis and erosive effect of pannus bone. This study provides ideas for searching potential targets of rheumatoid arthritis treatment and TCM drugs through network pharmacology.

[Heart failure caused by congenital hepatic hemangioma complicated with arteriovenous fistula in a neonate]. / æ–°ç”Ÿå„¿å ˆå¤©æ€§è‚è¡€ç®¡ç˜¤ä¼´åŠ¨é™è„‰ç˜˜å¯¼è‡´å¿ƒåŠŸèƒ½ä¸å ¨1例.

The three-day-old female infant was admitted to the hospital due to respiratory distress after birth. She was born premature at 36+2 weeks gestational age. Prenatal ultrasound suggested abnormal development of the fetal liver vessels, and she had dyspnea that required respiratory support after birth. Chest X-ray indicated an enlarged cardiac silhouette, and cardiac ultrasound revealed enlargement of the right atrium and right ventricle. Diagnosis of hepatic hemangioma with arteriovenous fistula was confirmed through liver ultrasound and abdominal enhanced CT. At 19 days old, she underwent ligation of the hepatic artery under general anesthesia, which led to an improvement in cardiac function and she was subsequently discharged. Genetic testing revealed a mutation in the ACVRL1 gene, which was inherited from the mother. The article primarily introduces a case of neonatal heart failure caused by hepatic hemangioma with arteriovenous fistula, and multi-disciplinary diagnosis and treatment of this disease.

[A rare case of neonatal-onset hepatic sinusoidal obstruction syndrome]. / æ–°ç”Ÿå„¿æœŸèµ·ç— çš„ç½•è§è‚çª¦é˜»å¡žç»¼åˆå¾1例.

A male infant, aged 1 month and 14 days, was admitted to the hospital due to abdominal distension lasting for 2 weeks and worsening for 3 days. The infant had a history of omphalitis. Physical examination revealed severe abdominal distension, prominent abdominal wall veins, hepatosplenomegaly, and massive ascites. There was a slight elevation in liver transaminase levels. Liver ultrasound and CT scans demonstrated the absence of visualization of the intrahepatic segment of the portal vein and the left, middle, and right veins of the liver, indicating occlusion of these vessels, along with surrounding fibrous hyperplasia. The clinical diagnosis was hepatic sinusoidal obstruction syndrome resulting from omphalitis. A large amount of bloody ascites developed after 12 days of hospitalization, resulting in hypovolemic shock and respiratory failure. The infant passed away following the family's decision to discontinue treatment. This article focuses on the diagnostic approach and multidisciplinary management of neonatal-onset hepatic sinusoidal obstruction syndrome, as well as provides insights into the differential diagnosis of hepatomegaly and ascites.

Drug Repurposing: Escitalopram attenuates acute lung injury by inhibiting the SIK2/ HDAC4/ NF-κB signaling cascade.

Acute lung injury (ALI) is a significant cause of morbidity and mortality worldwide. To search for a new treatment for acute lung injury, we investigated the effect of escitalopram on lipopolysaccharide (LPS)-induced ALI. Our results showed that escitalopram inhibited salt-inducible kinase 2 (SIK2) activity (IC50 = 6.36 ± 0.93 µM) and triggered histone deacetylase 4 (HDAC4) dephosphorylation. Following its dephosphorylation, HDAC4 translocated into the nucleus, promoted deacetylation and cytoplasmic shuttling of p65, thus inhibited LPS-induced pro-inflammatory cytokine production. Moreover, escitalopram markedly ameliorated the inflammatory responses, reduced neutrophils infiltration and attenuated LPS-induced pulmonary injury in mice. Taken together, we identified a previously unexplored role for escitalopram in SIK2/HDAC4/NF-κB pathway, therefore escitalopram may be considered as a new treatment for ALI.