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Abstract The spatiotemporal distribution of intangible cultural heritage in Fujian Province, China, and the factors that influence it were explored using multiple spatial scales. The samples include five batches of Chinese national-level and six batches of Chinese provincial-level intangible cultural heritage items, totaling 554. The samples involve city-scale, county-scale, and traditional dwellings, and the analysis uses various methods, such as gravity migration theory and the GeoDetector model. The results show that, in terms of historical timescales, the moving trajectory of the center of gravity of the intangible cultural heritage distribution in Fujian Province involves reciprocation from north to south, and the center moves south in time from the pre-Qin period to the modern period. Spatially, intangible cultural heritage in Fujian Province forms an overall aggregate pattern, among which traditional skills fall into an aggregate pattern; five categories, including traditional drama, fall into an aggregate-random pattern; and four categories, including traditional medicine, fall into a random pattern. The traditional art category and other intensive distribution areas are located in coastal areas, and the traditional dance category is scattered in northwestern Fujian Province. Experiments on the factors influencing intangible cultural heritage distribution were conducted at the city and county levels. At the city level, human geography factors, such as the resident population, urbanization rate, and gross domestic product, have a greater influence on distribution. At the county level, the influence of physical geographical factors clearly increases. The dominant factors for coastal cities are the normalized difference vegetation index (NDVI), average precipitation, and coastline, and that for inland cities is elevation. From the perspective of categories, the dominant factors of traditional music and Quyi are human geography factors, and those of other types of intangible cultural heritage are the synergistic effects of physical geography and human geography. The conclusions of this study are helpful for systematically protecting and developing the intangible cultural heritage industry and improving research theories and methodological systems of the spatiotemporal distribution and mechanism influencing intangible cultural heritage.

G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.

Abstract Membrane proteins are critical to biological processes and central to life sciences and modern medicine. However, membrane proteins are notoriously challenging to study, mainly owing to difficulties dictated by their highly hydrophobic nature. Previously, we reported QTY code, which is a simple method for designing water-soluble membrane proteins. Here, we apply QTY code to a transmembrane receptor, histidine kinase CpxA, to render it completely water-soluble. The designed CpxAQTY exhibits expected biophysical properties and highly preserved native molecular function, including the activities of (i) autokinase, (ii) phosphotransferase, (iii) phosphatase, and (iv) signaling receptor, involving a water-solubilized transmembrane domain. We probe the principles underlying the balance of structural stability and activity in the water-solubilized transmembrane domain. Computational approaches suggest that an extensive and dynamic hydrogen-bond network introduced by QTY code and its flexibility may play an important role. Our successful functional preservation further substantiates the robustness and comprehensiveness of QTY code.

ABSTRACT: Leg disorders have become increasingly common in broilers, leading to lower meat quality and major economic losses. This study evaluated the effects of dietary supplementation with Clostridium butyricum (C. butyricum) and 25-hydroxyvitamin D3 (25-OH-D3) on bone development by comparing growth performance, tibial parameters, Ca and P contents of tibial ash, bone development-related indicators’ level, and cecal short-chain fatty acids in Cobb broilers. All birds were divided into four treatment groups, which birds fed either a basal diet (Con), basal diet + 75 mg chlortetracycline/kg (Anti), basal diet + C. butyricum at 109 CFU/kg (Cb), basal diet + C. butyricum at 109 CFU/kg and 25-OH-D3 at 25 μg/kg (CbD), or basal diet + 25-OH-D3 at 25 μg/kg (CD). Our results suggest that the dietary supplementation in Cb, CbD, and CD significantly increased the body weight (BW) and average daily gain (ADG), and reduced the feed-to-weight ratio (F/G) at different stages of growth (P < 0.05). Dietary supplementation in Cb, CbD, and CD prolonged (P < 0.05) the behavioral responses latency-to-lie (LTL) time, reduced (P < 0.05) the levels of osteocalcin (BGP) and peptide tyrosine (PYY), and increased (P < 0.05) serotonin (5-HT) and dopamine (DA). Treatment with Cb increased (P < 0.05) the levels of acetic acid, isobutyric acid, butyric acid, and isovaleric acid compared with those in Con group. The cecal metagenome showed that Alistipes spp. were significantly more abundant in Cb, CbD, and CD groups (P < 0.05). A total of 12 metabolic pathways were significantly affected by supplementation, including the signaling pathways of glucagon, insulin, and PI3K-AKT; primary and secondary bile acid biosynthesis; and P-type Ca 2+ transporters (P < 0.05). Hence, the CbD supplementation modulates bone metabolism by regulating the mediators of gut–brain axis, which may inform strategies to prevent leg diseases and improve meat quality in broilers.

Abstract In recent years, as a promising way to realize digital transformation, digital twin shop-floor (DTS) plays an important role in smart manufacturing. The core feature of DTS is the synchronization. How to implement and maintain the synchronization is critical for DTS. However, there is still a lack of a common definition for synchronization in DTS. Besides, a systematic synchronization mechanism for DTS is strongly needed. This paper first summarizes the definition and requirements of synchronization in DTS, to clarify the understanding of synchronization in DTS. Then, a 5M synchronization mechanism for DTS is proposed, where 5M refers to multi-system data, multi-fidelity model, multi-resource state, multi-level state, and multi-stage operation. As a bottom-up synchronization mechanism, 5M synchronization mechanism for DTS has the potential to support DTS to achieve and maintain physical-virtual state synchronization, and to realize operation synchronization of DTS. The implementation methods of 5M synchronization mechanism for DTS are also introduced. Finally, the proposed synchronization mechanism is validated in a digital twin satellite assembly shop-floor, which proves the effectiveness and feasibility of the mechanism.

The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.

ABSTRACT Robust chassis are critical to facilitate advances in synthetic biology. This study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast growth rate is, in part, due to the efficient electron transport chain and key growth factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we used it to construct l-lactic acid producers for high lactate production. The development of genetically malleable yeast strains that grow faster than currently used strains may significantly enhance the uses of S. cerevisiae in biotechnology.IMPORTANCEYeast is known as an outstanding starting strain for constructing microbial cell factories. However, its growth rate restricts its application. A yeast strain XP, which grows fast in high concentrations of sugar and acidic environments, is revealed to demonstrate the potential in industrial applications. A toolbox was also built for its genetic manipulation including gene insertion, deletion, and ploidy transformation. The knowledge of its metabolism, which could guide the designing of genetic experiments, was generated with multi-omics analyses. This novel strain along with its toolbox was then tested by constructing an l-lactic acid efficient producer, which is conducive to the development of degradable plastics. This study highlights the remarkable competence of nonconventional yeast for applications in biotechnology.

Objective: To investigate the short-term efficacy and safety of different chemotherapy regimens combined with thalidomide, in the treatment of low-income patients with newly diagnosed HIV-associated diffuse large B-cell lymphoma. Methods: A retrospective analysis was performed on 42 patients with HIV-DLBCL who were admitted to the Infectious Diseases Department of Yunnan Provincial Infectious Diseases Hospital from January 2018 to December 2020. 14 cases (including 1 case in stage II and 13 cases in stage III/IV) were treated with R-CHOP, 24 cases (including 1 case in stage II and 23 cases in stage III/IV) were treated with R-DAEPOCH, and 4 cases (including 1 case in stage II and 3 cases in stage III/IV) were treated with EPOCH. All patients were treated with thalidomide. The ART regimen was adjusted. At least 1 and up to 6 intrathecal injections were given during chemotherapy, and cotrimoxazole was taken orally to prevent infection. The clinical efficacy was evaluated after 4 cycles of chemotherapy, and adverse events were evaluated at each cycle of chemotherapy. Results: All patients received 1–8 cycles of chemotherapy. CR (64.2 %) was achieved in 9 patients in R-CHOP group, and 5 patients died. In the R-DAEPOCH group, 17 patients achieved CR (70.8 %) and 7 died. In the EPOCH group, 2 patients reached CR (50 %) and 2 died. The main adverse reactions were grade II and above myelosuppression. Conclusion: Combined treatment with thalidomide can improve the prognosis of low-income patients with newly diagnosed HIV-DLBCL.

Human ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins and perform diverse functions. Many of them are associated with multidrug resistance that often results in cancer treatment with poor outcomes. Here, we present the structural bioinformatics study of six human ABC membrane transporters with experimentally determined cryo-electron microscopy (CryoEM) structures including ABCB7, ABCC8, ABCD1, ABCD4, ABCG1, ABCG5, and their AlphaFold2-predicted water-soluble QTY variants. In the native structures, there are hydrophobic amino acids such as leucine (L), isoleucine (I), valine (V), and phenylalanine (F) in the transmembrane alpha helices. These hydrophobic amino acids are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y). Therefore, these QTY variants become water soluble. We also present the superposed structures of native ABC transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with root mean square deviations between 1.064 and 3.413 Å despite significant (41.90–54.33%) changes to the protein sequence of the transmembrane domains. We also show the differences in hydrophobicity patches between the native ABC transporters and their QTY variants. We explain the rationale behind why the QTY membrane protein variants become water soluble. Our structural bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices and will likely further stimulate designs of water-soluble multispan transmembrane proteins and other aggregated proteins. The water-soluble ABC transporters may be useful as soluble antigens to generate therapeutic monoclonal antibodies for combating multidrug resistance in clinics.

Abstract Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database ( https://bio-gateway.aigene.org.cn/g/CrMP ), which aims to breach the gap between the two. Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. Five examples with varying transmembrane helices in different categories were used to demonstrate the feasibility. Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins.

Members of the Vibrionaceae family are predominantly fast-growing and halophilic microorganisms that have captured the attention of researchers owing to their potential applications in rapid biotechnology. Among them, Vibrio alginolyticus FA2 is a particularly noteworthy halophilic bacterium that exhibits superior growth capability. It has the potential to serve as a biotechnological platform for sustainable and eco-friendly open fermentation with seawater. To evaluate this hypothesis, we integrated the N-acetylglucosamine (GlcNAc) pathway into V. alginolyticus FA2. Seven nag genes were knocked out to obstruct the utilization of GlcNAc, and then 16 exogenous gna1s co-expressing with EcglmS were introduced to strengthen the flux of GlcNAc pathway, respectively. To further enhance GlcNAc production, we fine-tuned promoter strength of the two genes and inactivated two genes alsS and alsD to prevent the production of acetoin. Furthermore, unsterile open fermentation was carried out using simulated seawater and a chemically defined medium, resulting in the production of 9.2 g/L GlcNAc in 14 h. This is the first report for de-novo synthesizing GlcNAc with a Vibrio strain, facilitated by an unsterile open fermentation process employing seawater as a substitute for fresh water. This development establishes a basis for production of diverse valuable chemicals using Vibrio strains and provides insights into biomanufacture.

Abstract Underwater adhesive proteins secreted by organisms greatly inspires the development of underwater glue. However, except for specific proteins such as mussel adhesive protein, barnacle cement proteins, curli protein and their related recombinant proteins, it is believed that abundant common proteins cannot be converted into underwater glue. Here, we demonstrate that unfolded common proteins exhibit high affinity to surfaces and strong internal cohesion via amyloid-like aggregation in water. Using bovine serum albumin (BSA) as a model protein, we obtain a stable unfolded protein by cleaving the disulfide bonds and maintaining the unfolded state by means of stabilizing agents such as trifluoroethanol (TFE) and urea. The diffusion of stabilizing agents into water exposes the hydrophobic residues of an unfolded protein and initiates aggregation of the unfolded protein into a solid block. A robust and stable underwater glue can thus be prepared from tens of common proteins. This strategy deciphers a general code in common proteins to construct robust underwater glue from abundant biomass.

Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography–mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk’s initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.

The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I−III), with Group II further divided into five subgroups (IIa−IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.

Abstract Background Dietary bamboo leaf flavonoids (BLFs) are rarely used in poultry production, and it is unknown whether they influence meat texture profile, perceived color, or microstructure. Results A total of 720 one-day-old Arbor Acres broilers were supplemented with a basal diet with 20 mg bacitracin/kg, 50 mg BLFs/kg, or 250 mg BLFs/kg or without additions. Data showed that the dietary BLFs significantly (P

Since land resources are essential to human survival, the over-exploitation and unreasonable utilization of land threatens the sustainability of human society. This paper uses the well-developed Yangtze River Delta (YRD) region as a case study, and adopts an improved Mixed-cell Cellular Automata Model (MCCA) to simulate the potential utilization of land resources in 2025 and 2035. Then, the paper attempts to construct a comprehensive assessment system that integrates multiple indicators, and evaluates regional risk changes at a micro patch-cell level and a macro city. The results suggest that (1) The utilization of land resources varies greatly in the YRD region from 2020 to 2035. While Shanghai will continue to make use of available built up land resources, the majority of land resources in Jiangsu Province will shift away from being agricultural in nature. Since forests make up a majority of the land resources in Zhejiang Province, and forests and agricultural land make up a majority of land resources in Anhui Province, the change in land utilization in these two provinces will be more gradual. (2) Changes in land utilization are also likely to cause ecological risks. The risk level in Shanghai is the highest, it is relatively high in Zhejiang but is likely to decrease, relatively low in Jiangsu but likely to increase, and Anhui has the lowest risk level. (3) The K-means clustering method obtained three ecological risk zones of the YRD, and the overall risk level is the highest in the central-eastern zoning ③, followed by the southern zoning ②, and the lowest in the northern zoning ①. Furthermore, the agglomeration pattern of the three zones transforms from L-L to H-H. (4) This paper puts forward corresponding suggestions and countermeasures for four aspects, including the strengthening of agricultural land protection, the regulation of built-up land use expansion, the coordination of an all-rounded approach of urban development, and the fostering of regional sustainable development, in hopes of optimizing land usage and alleviating ecological risk levels. Scientific estimations of potential ecological risks are critical to avoiding future ecological crises thus contributing to more sustainability.

Composite materials are widely used in many fields due to their excellent properties. Quality defects in composite materials can lead to lower quality components, creating potential risk of accidents. Experimental and simulation methods are commonly used to predict the quality of composite materials. However, it is difficult to predict the quality of composite materials accurately due to the uncertain curing environment and incomplete feature space. To address this problem, a digital twin (DT) visual model of a composite material is first constructed. Then, a static autoclave DT virtual model is coupled with a variable composite material DT virtual model to construct a model of the curing process. Features are added to the proposed model by generating simulated data to enhance the quality prediction. An extreme learning machine (ELM) for quality prediction is trained with the generated data. Finally, the effectiveness of the proposed method is verified through result analysis.

With rapid development of Artificial Intelligence (AI), researchers have found many bioinspired AI applications, such as bioinspired images and speech processing, which can increase accuracy [...]

Herein, the use of biomolecules is reviewed as raw materials for creating functional responsive materials with a variety of tunable properties, including physicochemical and mechanical properties. Through self‐assembly/coassembly, self‐powered smart devices can be designed, which aim to create efficient and stable transformation systems within existing energy relations. These systems can respond to various chemical or physical stimuli, triggering reassembly and completing potential energy conversion through conformational changes at the molecular and mesoscopic scales. This energy conversion provides the necessary energy for macroscopic feedback behavior. Herein, bionic devices are presented that can perform energy conversion completely and autonomously and discuss the mechanism of energy conversion between different chemical potentials, kinetic, or thermal energies.

BackgroundReports on Lenvatinib-based therapies show promising treatment outcomes for patients with unresectable hepatocellular carcinoma (uHCC). However, the effect and safety of Lenvatinib-based therapies still need to be further studies.MethodsThis was a retrospective, single-center study on the safety and treatment efficacy of Lenvatinib-based combination therapies for uHCC Patients. The primary endpoints were progression-free survival (PFS) and overall survival (OS). The secondary endpoints were progressive disease (PD), stable disease (SD), partial response (PR), and complete response (CR).ResultsOf 91 patients, there were 16 females and 75 males with uHCC who received systemic therapies based on Lenvatinib in our center. Forty-six patients (50.5%) received Lenvatinib combined with PD-1 antibody treatment. All these patients also received local therapy with the exception of 2 patients. The remaining 36 patinets received Lenvatinib combined with transcatheter arterial chemoembolization (TACE), 1 patient treated Lenvatinib combined with radiotherapy, 8 patients received Lenvatinib alone. At a median treatment time of 8 months, the objective response rate (ORR) of the entire cohort was 58.2% (53 patients), including 7 patients with CR and 46 patients with PR. 21 patients (23.1%) had SD. The disease control rate (DCR) of all patients was 81.3% (74 patients). However, 17 patients (18.7%) developed PD. The 1- and 2-year cumulative OS rates for the entire cohort were 66.8% and 39.3%, while the corresponding PFS rates were 38.0% and 17.1%, respectively. Univariate and multivariate Cox regression analysis revealed multiple tumor sites to be an independent OS risk factor for uHCC patients (HR=2.204, 95% CI=1.104-4.399, P=0.025). The most frequently reported adverse events in all patients were AST elevation (51.6%), followed by hypertension (33.0%), ALT elevation (26.4%), and decreased appetite (25.3%). After a combination treatment of Lenvatinib-based therapies, 15 patients met the criteria for salvage liver resection and underwent down-staging hepatectomy with a curative intent. The combination of PD-1 treatment was not very effective in improving the prognosis of uHCC patients treated with Lenvatinib combined with TACE.ConclusionOur study demonstrated that a proportive of patients benefited from Lenvatinib-based combination therapies with manageable safety profiles, allowing these patients to undergo downstaging surgery with curative intent.

Summary: Synthetic biology, relying on Design-Build-Test-Learn (DBTL) cycle, aims to solve medicine, manufacturing, and agriculture problems. However, the DBTL cycle’s Learn (L) step lacks predictive power for the behavior of biological systems, resulting from the incompatibility between sparse testing data and chaotic metabolic networks. Herein, we develop a method, “RespectM,” based on mass spectrometry imaging, which is able to detect metabolites at a rate of 500 cells per hour with high efficiency. In this study, 4,321 single cell level metabolomics data were acquired, representing metabolic heterogeneity. An optimizable deep neural network was applied to learn from metabolic heterogeneity and a “heterogeneity-powered learning (HPL)” based model was trained as well. By testing the HPL based model, we suggest minimal operations to achieve high triglyceride production for engineering. The HPL strategy could revolutionize rational design and reshape the DBTL cycle.

Abstract Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chemo-sensitivity. Here we report the study of 13 human solute carrier membrane transporters using the highly accurate AlphaFold2 predictions of 3D protein structures. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane alpha-helices. These hydrophobic amino acids L, I, V, F are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T) and tyrosine (Y), thus the QTY code. Therefore, these QTY variant transporters become water-soluble without requiring detergents. We present the superposed structures of these native solute carrier transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with RMSD ~ 1 Å– 46% protein sequence substitutions in transmembrane alpha-helices. We also show the differences of surface hydrophobicity between the native solute carrier transporters and their QTY variants. Our study may further stimulate designs of water-soluble transmembrane proteins and other aggregated proteins for drug discovery and biotechnological applications.

Summary: l-Alanine is an important amino acid widely used in food, medicine, materials, and other fields. Here, we develop Bacillus licheniformis as an efficient l-alanine microbial cell factory capable of realizing high-temperature fermentation. By enhancing the glycolytic pathway, knocking out the by-product pathways and overexpressing the thermostable alanine dehydrogenase, the engineered B. licheniformis strain BLA3 produced 93.7 g/L optically pure l-alanine at 50°C. Subsequently, d-alanine dependence of an alanine racemase-deficient strain is relieved by adaptive laboratory evolution, implying that a dormant alternative pathway for d-alanine synthesis is activated in the evolved strain. The d-amino acid aminotransferase Dat1 is shown to be a key enzyme in the dormant alternative pathway. Molecular mechanism of the d-alanine dependence is revealed via mutational analysis. This study demonstrates a novel technology for high-temperature l-alanine production and shows that activating dormant metabolic pathway(s) is an effective strategy of metabolic engineering.

Inhibiting α-amylase can lower postprandial blood glucose levels and delay glucose absorption, offering an effective approach for the development of antidiabetic diets. In this study, an active constituent with inhibitory activity against α-amylase was isolated and purified by bioassay-guided fractionation from Carya cathayensis Sarg. peel (CCSP). The active constituent was identified by NMR and Q-Exactive Orbitrap Mass Spectrometry as 5-O-p-coumaroylquinic acid (5-CQA). 5-CQA possessed strong inhibitory activity against α-amylase, with an IC50 value of 69.39 µM. In addition, the results of the kinetic study indicated that 5-CQA was a potent, reversible, noncompetitive inhibitor against α-amylase. The findings indicate that 5-CQA derived from CCSP has potential as a novel inhibitor against α-amylase, which can help mitigate postprandial blood sugar spikes, making it suitable for inclusion in antidiabetic diets.

Synechococcus, a type of ancient photosynthetic cyanobacteria, is crucial in modern carbon-negative synthetic biology due to its potential for producing bioenergy and high-value products. With its high biomass, fast growth rate, and established genetic manipulation tools, Synechococcus has become a research focus in recent years. Abundant germplasm resources have been accumulated from various habitats, including temperature and salinity conditions relevant to industrialization. In this study, a comprehensive analysis of complete genomes of the 56 Synechococcus strains currently available in public databases was performed, clarifying genetic relationships, the adaptability of Synechococcus to the environment, and its reflection at the genomic level. This was carried out via pan-genome analysis and a detailed comparison of the functional gene groups. The results revealed an open-genome pattern, with 275 core genes and variable genome sizes within these strains. The KEGG annotation and orthology composition comparisons unveiled that the cold and thermophile strains have 32 and 84 unique KO functional units in their shared core gene functional units, respectively. Each KO functional unit reflects unique gene families and pathways. In terms of salt tolerance and comparative genomics, there are 65 unique KO functional units in freshwater-adapted strains and 154 in strictly marine strains. By delving into these aspects, our understanding of the metabolic potential of Synechococcus was deepened, promoting the development and industrial application of cyanobacterial biotechnology.

Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the oligomerization patterns of many chemokine receptors remain poorly understood. Furthermore, several chemokine receptors have highly truncated isoforms whose functional role is not yet clear. Here, we computationally show homo- and heterodimerization patterns of four human chemokine receptors, namely CXCR2, CXCR7, CCR2, and CCR7, along with their interaction patterns with their respective truncated isoforms. By combining the neural network-based AlphaFold2 and physics-based protein–protein docking tool ClusPro, we predicted 15 groups of complex structures and assessed the binding affinities in the context of atomistic molecular dynamics simulations. Our results are in agreement with previous experimental observations and support the dynamic and diverse nature of chemokine receptor dimerization, suggesting possible patterns of higher-order oligomerization. Additionally, we uncover the strong potential of truncated isoforms to block homo- and heterodimerization of chemokine receptors, also in a dynamic manner. Our study provides insights into the dimerization patterns of chemokine receptors and the functional significance of their truncated isoforms.

Asthenopia is a syndrome based on the symptoms of eye discomfort that has become a chronic disease that interferes with and harms people’s physical and mental health. Lutein is an internationally recognized “eye nutrient”, and studies have shown that it can protect the retina and relieve visual fatigue. In this study, lutein was extracted from marigold (Tagetes erecta L.) and saponified. The purified lutein concentration measured by HPLC was 50.12 mg/100 g. Then, purified lutein was modified to be water-soluble by nanoscale modification and microencapsulation technology. Water-soluble lutein was then mixed with a leaching solution of Chinese wolfberry and chrysanthemum to make a functional beverage. The effects of this beverage on hepatic antioxidant enzymes and the alleviation of visual fatigue in a rat model of diabetes were investigated for 4 weeks. Lutein intake of 0.72 (medium-lutein beverage group) and 1.44 mg/mL (high-lutein beverage group) relieved visual fatigue, ameliorated turbidity symptoms of impaired crystalline lenses, reduced hepatic MDA concentration, increased hepatic GSH concentration, and significantly increased the activities of the hepatic antioxidant enzymes SOD, CAT, GSH-Px, and GR in rats. These data suggest that a lutein-rich beverage is an effective and harmless way to increase the total anti-oxidation capacity of lenses and alleviate visual fatigue.

Abstract The effect of crystallography on transgranular chloride-induced stress corrosion cracking (TGCISCC) of arc welded 304L austenitic stainless steel is studied on >300 grains along crack paths. Schmid and Taylor factor mismatches across grain boundaries (GBs) reveal that cracks propagate either from a hard to soft grain, which can be explained merely by mechanical arguments, or soft to hard grain. In the latter case, finite element analysis reveals that TGCISCC will arrest at GBs without sufficient mechanical stress, favorable crystallographic orientations, or crack tip corrosion. GB type does not play a significant role in determining TGCISCC cracking behavior nor susceptibility. TGCISCC crack behaviors at GBs are discussed in the context of the competition between mechanical, crystallographic, and corrosion factors.

Summary 3, 4‐Dihydroxyphenyl‐l‐alanine (l‐DOPA) is a compound of high medical value and is considered effective as a treatment for Parkinson’s disease. Currently, bioproduction of l‐DOPA is mainly carried out by whole‐cell catalysis mediated by recombinant Escherichia coli carrying heterogeneous tyrosine phenol lyase. Vibrio natriegens is increasingly attracting attention owing to its superiority, including extremely rapid growth and high soluble protein expression capacity. In this study, we attempt to develop an efficient whole‐cell catalyst for l‐DOPA production using V. natriegens as the chassis. The maximum soluble protein expression by V. natriegens was accomplished in 4 h at 37°C, which was equivalent to that achieved by E. coli in 16 h at 16°C. Furthermore, the maximum productivity reached over 10.0 g l−1 h−1 in the early stage of biocatalysis, nearly two‐fold higher than previously reported. Approximately 54.0 g l−1 l‐DOPA was obtained with a catechol conversion rate greater than 95%. In conclusion, V. natriegens displays advantages, including rapid protein expression and catalytic rate in the catalysis process for l‐DOPA production. These findings strongly suggest that V. natriegens has remarkable potential as a whole‐cell catalysis chassis for the production of valuable chemicals.

Abstract Background During fermentation, industrial microorganisms encounter multiple stresses that inhibit cell growth and decrease fermentation yields, in particular acid stress, which is due to the accumulation of acidic metabolites in the fermentation medium. Although the addition of a base to the medium can counteract the effect of acid accumulation, the engineering of acid-tolerant strains is considered a more intelligent and cost-effective solution. While synthetic biology theoretically provides a novel approach for devising such tolerance modules, in practice it is difficult to assemble stress-tolerance modules from hundreds of stress-related genes. Results In this study, we designed a set of synthetic acid-tolerance modules for fine-tuning the expression of multi-component gene blocks comprising a member of the proton-consuming acid resistance system (gadE), a periplasmic chaperone (hdeB), and reactive oxygen species (ROS) scavengers (sodB and katE). Directed evolution was used to construct an acid-responsive asr promoter library, from which four variants were selected and used in the synthetic modules. The module variants were screened in a stepwise manner under mild acidic conditions (pH 5–6), first by cell growth using the laboratory Escherichia coli strain MG1655 cultured in microplates, and then by lysine production performance using the industrial lysine-producing E. coli strain MG1655 SCEcL3 cultured first in multiple 10-mL micro-bioreactors, and then in 1.3-L parallel bioreactors. The procedure resulted in the identification of a best strain with lysine titer and yield at pH 6.0 comparable to the parent strain at pH 6.8. Conclusion Our results demonstrate a promising synthetic-biology strategy to enhance the growth robustness and productivity of E. coli upon the mildly acidic conditions, in both a general lab strain MG1655 and an industrial lysine-producing strain SCEcL3, by using the stress-responsive synthetic acid-tolerance modules comprising a limited number of genes. This study provides a reliable and efficient method for achieving synthetic modules of interest, particularly in improving the robustness and productivity of industrial strains.

BackgroundThe differences in short- and long-term outcome between laparoscopic liver resection (LLR) and open liver resection (OLR) for BCLC stage A large hepatocellular carcinoma (HCC) in difficult segments (I, IVa, VII, VIII) remain unclear. This PSM two-centre study aimed to compare perioperative and long-term survival outcomes of LLR with OLR for this HCC.MethodsHCC patients with BCLC stage A who underwent OLR or LLR in two medical centres were enrolled in the study. PSM analysis was performed to match patients between the LLR cohort and OLR cohort. Survival was analysed based on the Kaplan–Meier method. Independent risk factors were identified by Cox regression.ResultsAfter PSM, 35 patients remained in the LLR cohort, and 84 remained in the OLR cohort. Patients in the LLR cohort had more intraoperative blood loss (p=0.036) and shorter hospital stays after surgery (p

Using computer simulation tools such as finite element analysis (FEA) to perform material stress analysis is a common design method in engineering practice. In order to model more realistic real‐world systems, simulation models have become more complex, and calculation becomes more expensive as a result. The rise of artificial intelligence technologies has made it possible to integrate deep learning methods and material stress analysis. Herein, FEA software is employed to obtain a large number of analysis cases as training samples and uses a fully connected neural network and long‐short‐term memory neural network as surrogate models, which can predict the stress distribution and stress sequence in the process of the bullet impacting target plates with different materials. These models can give results similar to FEA with 92.19% and 92.41% accuracy, respectively. The experimental results show that the deep learning surrogate models have great potential in material stress analysis.

Summary: The host-guest incompatibility between a production host and non-native enzymes has posed an arduous challenge for synthetic biology, particularly between mesophile-derived enzymes and a thermophilic chassis. In the present study, we develop a thermophilic enzyme mining strategy comprising an automated co-evolution-based screening pipeline (http://cem.sjtu.edu.cn), computation-based enzyme characterization, and gene synthesis-based function validation. Using glucosamine-6-phosphate acetyltransferase (GNA1) as an example, we successfully mined four novel GNA1s with excellent thermostabilities and catalytic performances. Calculation and analysis based on AlphaFold2-generated structures were also conducted to uncover the mechanism underlying their excellent properties. Finally, our mined GNA1s were used to enable the high-temperature N-acetylglucosamine (GlcNAc) production with high titers of up to 119.3 g/L, with the aid of systems metabolic engineering and temperature programming. This study demonstrates the effectiveness of the enzyme mining strategy, highlighting the application prospects of mining new enzymes from massive databases and providing an effective solution for tackling host-guest incompatibility.

Strain glass is a new glassy state characterized by frozen ferroelastic nanodomains. Here, the authors discover a low-temperature feature in the specific heat of a strain glass, which is similar to the well-known boson peak anomaly of structural glasses, but cannot be explained by existing mechanisms.

Background Despite the survival benefits observed with immune checkpoint blockade (ICB) treatment—programmed cell death-1/programmed cell death ligand-1 (PD-1/PD-L1), many patients with cancer have not benefited from these agents because of impaired antigen presentation and other resistance mechanisms. To overcome resistance to checkpoint therapy, we designed bispecific antibodies (BsAbs) targeting CD89 and tumor antigens. We demonstrated their immunomodulatory efficacy as a separate treatment strategy or combined with immune checkpoint inhibitors.Methods We have previously generated a heterodimeric one-arm IgG1 Fc-based bispecific antibody. For animal efficacy studies, murine tumors in a humanized transgenic mice model were used to determine the effects of CD89-bispecific antibodies on antigen presentation and immune cell recruitment. The efficacy of the CD89 bispecific antibody against tumors resistant to pembrolizumab was evaluated in double-transgenic mice.Results BsAbs targeting CD89 on tumor-associated macrophages (TAMs) increased the ratio of M1:M2 and activated the antigen presentation, leading to increased cytotoxic T cell-mediated tumor regression. CD89-BsAbs also potentiated a combinational antitumor effect with PD-1/PD-L1 inhibitors and overcame the ICB resistance by augmenting cytotoxic T-cell infiltration and reshaping tumor immune microenvironment. In an hCD89/hPD-1 double transgenic mouse model engrafted with pembrolizumab-resistant B16-HER2 tumor cells, the HER2-CD89 bispecific antibody potently inhibited tumor growth.Conclusions CD89 BsAbs targeting tumor antigens and TAMs controlled tumor growth in animal models by improving antigen presentation and T-cell infiltration. Our results suggest a general strategy for overcoming resistance to ICB.

Summary: The misuse of petroleum-based plastics has resulted in serious environmental pollution and resource wastage. Biodegradable plastics can be used as green substitutes for traditional plastics. Here, we discuss the feasibility and technical bottlenecks in developing microbial cell factories for the production of biodegradable plastics from lignocellulosic wastes. First, we introduce the basic properties of the main biodegradable plastics on the market, including poly(lactic acid), poly(hydroxyalkanoate), and poly(butylene adipate-co-terephthalate). We then demonstrate the feasibility of synthesizing petroleum-based biodegradable plastic monomers from bio-based raw materials and propose strategies to further advance their commercial production through metabolic engineering and synthetic biology. We also analyze the main challenges facing the current development of bio-based biodegradable plastic biosynthesis technology. Finally, we discuss the current major lignocellulose bioconversion processes and explore way to further improve the utilization efficiency of the main carbohydrates in lignocellulosic hydrolysates by microorganisms, from the perspectives of sugar transport, sugar assimilation, and carbon catabolite inhibition.

The Polarization CrossFire (PCF) suite onboard the Chinese GaoFen-5(02) satellite has been sophisticatedly composed by the Particulate Observing Scanning Polarimeter (POSP) and the Directional Polarimetric Camera (DPC). Among them, DPC is a multi-angle sequential measurement polarization imager, while POSP is a cross-track scanning simultaneous polarimeter with corresponding radiometric and polarimetric calibrators, which can theoretically be used for cross comparison and calibration with DPC. After the data preprocessing of these two sensors, we first select local homogeneous cluster scenes by calculating the local variance-to-mean ratio in DPC’s Level 1 product projection grids to reduce the influence of scale differences and geometry misalignment between DPC and POSP. Then, taking the observation results after POSP data quality assurance as the abscissa and taking the DPC observation results under the same wavelength band and geometric conditions as the same ordinate, a two-dimensional radiation/polarization feature space is established. Results show that the normalized top of the atmosphere (TOA) radiances of DPC and POSP processed data at the nadir are linearly correlated. The normalized TOA radiance root mean square errors (RMSEs) look reasonable in all common bands. The DPC and POSP normalized radiance ratios in different viewing zenith angle ranges at different times reveal the temporal drift of the DPC relative radiation response. The RMSEs, mean absolute errors (MAEs), relative errors (REs), and scatter percentage of DPC degree of linear polarization (DoLP) falling within the expected error (EE = ±0.02) of POSP measured DoLP are better than 0.012, 0.009, 0.066, and 91%, respectively.

The application of intelligence to manufacturing has emerged as a compelling topic for researchers and industries around the world. However, different terminologies, namely smart manufacturing (SM) and intelligent manufacturing (IM), have been applied to what may be broadly characterized as a similar paradigm by some researchers and practitioners. While SM and IM are similar, they are not identical. From an evolutionary perspective, there has been little consideration on whether the definition, thought, connotation, and technical development of the concepts of SM or IM are consistent in the literature. To address this gap, the work performs a qualitative and quantitative investigation of research literature to systematically compare inherent differences of SM and IM and clarify the relationship between SM and IM. A bibliometric analysis of publication sources, annual publication numbers, keyword frequency, and top regions of research and development establishes the scope and trends of the currently presented research. Critical topics discussed include origin, definitions, evolutionary path, and key technologies of SM and IM. The implementation architecture, standards, and national focus are also discussed. In this work, a basis to understand SM and IM is provided, which is increasingly important because the trend to merge both terminologies rises in Industry 4.0 as intelligence is being rapidly applied to modern manufacturing and human–cyber–physical systems.