CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.

Flux balance analysis (FBA) is an important method for calculating optimal pathways to produce industrially important chemicals in genome-scale metabolic models (GEMs). However, for biologists, the requirement of coding skills poses a significant obstacle to using FBA for pathway analysis and engineering target identification. Additionally, a time-consuming manual drawing process is often needed to illustrate the mass flow in an FBA-calculated pathway, making it challenging to detect errors or discover interesting metabolic features. To solve this problem, we developed CAVE, a cloud-based platform for the integrated calculation, visualization, examination and correction of metabolic pathways. CAVE can analyze and visualize pathways for over 100 published GEMs or user-uploaded GEMs, allowing for quicker examination and identification of special metabolic features in a particular GEM. Additionally, CAVE offers model modification functions, such as gene/reaction removal or addition, making it easy for users to correct errors found in pathway analysis and obtain more reliable pathways. With a focus on the design and analysis of optimal pathways for biochemicals, CAVE complements existing visualization tools based on manually drawn global maps and can be applied to a broader range of organisms for rational metabolic engineering. CAVE is available at https://cave.biodesign.ac.cn/.

Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis.

Enzymes play a crucial role in various industrial production and pharmaceutical developments, serving as catalysts for numerous biochemical reactions. Determining the optimal catalytic temperature (Topt) of enzymes is crucial for optimizing reaction conditions, enhancing catalytic efficiency, and accelerating the industrial processes. However, due to the limited availability of experimentally determined Topt data and the insufficient accuracy of existing computational methods in predicting Topt, there is an urgent need for a computational approach to predict the Topt values of enzymes accurately. In this study, using phosphatase (EC 3.1.3.X) as an example, we constructed a machine learning model utilizing amino acid frequency and protein molecular weight information as features and employing the K-nearest neighbors regression algorithm to predict the Topt of enzymes. Usually, when conducting engineering for enzyme thermostability, researchers tend not to modify conserved amino acids. Therefore, we utilized this machine learning model to predict the Topt of phosphatase sequences after removing conserved amino acids. We found that the predictive model's mean coefficient of determination (R2) value increased from 0.599 to 0.755 compared to the model based on the complete sequences. Subsequently, experimental validation on 10 phosphatase enzymes with undetermined optimal catalytic temperatures shows that the predicted values of most phosphatase enzymes based on the sequence without conservative amino acids are closer to the experimental optimal catalytic temperature values. This study lays the foundation for the rapid selection of enzymes suitable for industrial conditions.

Thermodynamic Phase Transition of Three-Dimensional Solid Additives Guiding Molecular Assembly for Efficient Organic Solar Cells.

Fine-tuning the thermodynamic self-assembly of molecules via volatile solid additives has emerged to be an effective way to construct high-performance organic solar cells. Here, three-dimensional structured solid molecules have been designed and applied to facilitate the formation of organized molecular assembly in the active layer. By means of systematic theory analyses and film-morphology characterizations based on four solid candidates, we preselected the optimal one, 4-fluoro-N,N-diphenylaniline (FPA), which possesses good volatility and strong charge polarization. The three-dimensional solids can induce molecular packing in active layers via strong intermolecular interactions and subsequently provide sufficient space for the self-reassembly of active layers during the thermodynamic transition process. Benefitting from the optimized morphology with improved charge transport and reduced energy disorder in the FPA-processed devices, high efficiencies of over 19 % were achieved. The strategy of three-dimensional additives inducing ordered self-assembly structure represents a practical approach for rational morphology control in highly efficient devices, contributing to deeper insights into the structural design of efficient volatile solid additives.

Electroluminescent white light-emitting diodes with cadimum-free Cu-In-Zn-S nanocrystals sandwiched between two TFB layers.

A high color rendering index (CRI) and stable spectra under different voltages are important parameters for large-area planar light sources. However, the spectrum of most electroluminescent white light-emitting diodes (el-WLEDs) with a single emissive layer (EML) varies with a changing voltage. Herein, an el-WLED is fabricated based on Cd-free Cu-In-Zn-S (CIZS)/ZnS nanocrystals (NCs) and poly [(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4'-(N-(p-butylphenyl))diphenylamine)] (TFB) as double EMLs, which exhibit white-light emission with a high CRI value of 91 and commission internationale de l'éclairage (CIE) color coordinates of (0.33, 0.33). Meanwhile, it has a stable spectrum under voltage up to 7 V and a maximum luminance up to 679 cd/m2 with a low turn-on voltage of 2.2 V. This work provides a foundation for Cd-free el-WLEDs with high CRI and stable spectra.

Characterization of genomic alterations in Chinese colorectal cancer patients with liver metastases.

BACKGROUND: The exploration of genomic alterations in Chinese colorectal liver metastasis (CRLM) is limited, and corresponding genetic biomarkers for patient's perioperative management are still lacking. This study aims to understand genome diversification and complexity that developed in CRLM. METHODS: A custom-designed IDT capture panel including 620 genes was performed in the Chinese CRLM cohort, which included 396 tumor samples from metastatic liver lesions together with 133 available paired primary tumors. RESULTS: In this Chinese CRLM cohort, the top-ranked recurrent mutated genes were TP53 (324/396, 82%), APC (302/396, 76%), KRAS (166/396, 42%), SMAD4 (54/396, 14%), FLG (52/396, 13%) and FBXW7 (43/396, 11%). A comparison of CRLM samples derived from left- and right-sided primary lesions confirmed that the difference in survival for patients with different primary tumor sites could be driven by variations in the transforming growth factor ß (TGF-ß), phosphatidylinositol 3-kinase (PI3K) and RAS signaling pathways. Certain genes had a higher variant rate in samples with metachronous CRLM than in samples with simultaneous metastasis. Overall, the metastasis and primary tumor samples displayed highly consistent genomic alterations, but there were some differences between individually paired metastases and primary tumors, which were mainly caused by copy number variations. CONCLUSION: We provide a comprehensive depiction of the genomic alterations in Chinese patients with CRLM, providing a fundamental basis for further personalized therapy applications.

Melatonin promotes secondary hair follicle development of early postnatal cashmere goat and improves cashmere quantity and quality by enhancing antioxidant capacity and suppressing apoptosis.

Development of secondary hair follicles in early postnatal cashmere goats may be adversely affected by reactive oxygen species which cause oxidative stress. Because melatonin is a potent antioxidant and scavenger of free radicals, this study explored the effects of melatonin on secondary hair follicle development and subsequent cashmere production. It was found that the initiation of new secondary follicles in early postnatal Inner Mongolian cashmere goats of both melatonin-treated and control goats occurred in the first 10 weeks of age. Melatonin promoted the initiation and maturation of secondary follicles and increased their population. Importantly, the beneficial effect of melatonin on secondary follicle population remained throughout life. As a result, melatonin increased cashmere production and improved its quality in terms of reduced fiber diameter. The mechanisms underlying the role of melatonin on secondary follicle development included the enhancement of activities of antioxidant enzymes, for example, superoxide dismutase and glutathione peroxidase (GSH-Px), elevated total antioxidant capacity, and upregulated anti-apoptotic Bcl-2 expression and downregulated expression of the pro-apoptotic proteins, Bax and caspase-3. These results reveal that melatonin serves to promote secondary hair follicle development in early postnatal cashmere goats and expands our understanding of melatonin application in cashmere production. Melatonin treatment led to an increase in both the quantity and quality of cashmere fiber. This increased the textile value of the fibers and provided economic benefit.

Udder skin surface temperature variation pre- and post- milking in dairy cows as determined by infrared thermography.

The objectives of the research reported in this Research Communication were to compare the variation of hind quarter skin surface temperature pre- and post- milking in dairy cows and to determine the optimal time to capture images by infrared thermography for improving the sensitivity and specificity of mastitis detection in dairy cows. Hind quarter infrared images of 102 Holstein dairy cows were captured from the caudal view by an infrared camera pre-milking and post-milking. The udder skin surface temperature was measured with the help of the image processing software. No significant difference was found between the left and right quarter skin surface temperature pre- and post- milking. The hind quarter skin surface temperature pre-milking was not significantly influenced by milk yield, but exhibited a rising trend along with the increase of milk yield. The hind quarter skin surface temperature post-milking was significantly influenced by milk yield. This leads us to conclude that the sensitivity and specificity of IRT in mastitis detection may be influenced by milk yield and it may be better to capture the infrared images of cow udders pre-milking.

Dye-Incorporated Polynaphthalenediimide Acceptor for Additive-Free High-Performance All-Polymer Solar Cells.

All-polymer solar cells (all-PSCs) can offer unique advantages for applications in flexible devices, and naphthalene diimide (NDI)-based polymer acceptors are the widely used polymer acceptors. However, their power conversion efficiency (PCE) still lags behind that of state-of-the-art polymer solar cells, due to low light absorption, suboptimal energy levels and the strong aggregation of the NDI-based polymer acceptor. Herein, a rhodanine-based dye molecule was introduced into the NDI-based polymer acceptor by simple random copolymerization and showed an improved light absorption coefficient, an up-shifted lowest unoccupied molecular orbital level and reduced crystallization. Consequently, additive-free all-PSCs demonstrated a high PCE of 8.13 %, which is one of the highest performance characteristics reported for all-PSCs to date. These results indicate that incorporating a dye into the n-type polymer gives insight into the precise design of high-performance polymer acceptors for all-PSCs.

The complete genome of a viable archaeum isolated from 123-million-year-old rock salt.

Live microbes have been isolated from rock salt up to Permian age. Only obligatory cellular functions can be performed in halite-buried cells. Consequently, their genomic sequences are likely to remain virtually unchanged. However, the available sequence information from these organisms is scarce and consists of mainly ribosomal 16S sequences. Here, live archaea were isolated from early Cretaceous (∼ 123 million years old) halite from the depth of 2000 m in Qianjiang Depression, Hubei Province, China. The sample was radiologically dated and subjected to rigorous surface sterilization before microbe isolation. The isolates represented a single novel species of Halobacterium, for which we suggest the name Halobacterium hubeiense, type strain Hbt. hubeiense JI20-1. The species was closely related to a Permian (225-280 million years old) isolate, Halobacterium noricense, originating from Alpine rock salt. This study is the first one to publish the complete genome of an organism originating from surface-sterilized ancient halite. In the future, genomic data from halite-buried microbes can become a key factor in understanding the mechanisms by which these organisms are able to survive in harsh conditions deep underground or possibly on other celestial bodies.

Transcriptome analysis reveals that constant heat stress modifies the metabolism and structure of the porcine longissimus dorsi skeletal muscle.

Exposure to high ambient temperatures is detrimental to pig rearing and porcine meat quality. Deep molecular sequencing allows for genomic characterization of porcine skeletal muscles and helps understand how the genomic landscape may impact meat quality. To this end, we performed mRNA-seq to molecularly dissect the impact of heat stress on porcine skeletal muscles, longissimus dorsi. Sixteen castrated, male DLY pigs [which are crossbreeds between Duroc (D) boars and Landrace (L) × Yorkshire (Y) sows, 79.0 ± 1.5 kg BW] were evenly split into two groups that were subjected to either control (CON) (22 °C; 55 % humidity) or constant heat stress (H30; 30 °C; 55 % humidity) conditions for 21 days. Seventy-eight genes were found to be differentially expressed, of which 37 were up-regulated and 41 were down-regulated owing to constant heat stress. We predicted 5247 unknown genes and 6108 novel transcribed units attributed to alternative splicing (AS) events in the skeletal muscle. Furthermore, 30,761 and 31,360 AS events were observed in the CON and H30 RNA-seq libraries, respectively. The differentially expressed genes in the porcine skeletal muscles were involved in glycolysis, lactate metabolism, lipid metabolism, cellular defense, and stress responses. Additionally, the expression levels of these genes were associated with variations in meat quality between the CON and H30 groups, indicating that heat stress modulated genes crucial to skeletal muscle development and metabolism. Our transcriptomic analysis provides valuable information for understanding the molecular mechanisms governing porcine skeletal muscle development. Such insights may lead to innovative strategies to improve meat quality of pigs under heat stress.

Keratin 8 is a novel autoantigen of rheumatoid arthritis.

OBJECTIVE: This research aims to verify Keratin 8 (K8) as a specific autoantigen in rheumatoid arthritis (RA). METHODS: First, total RNA was extracted from HaCaT cell to obtain cDNA by inverse transcription. Then, PCR was performed to amplify corresponding gene by K8 primers. Next, cloning, expression, and purification technology were used to obtain the recombinant human K8 (rhK8). At last, the purified rhK8, after identified by mass spectrometer, was used to perform further disease-related Western blotting and ELISA test with real clinical samples. RESULTS: Purified rhK8 was successfully obtained and then Western blotting confirmed antigenicity of K8 in rheumatoid arthritis. The reactivity of serum IgG against rhK8 was further detected in 34 of 50 RA patients (68%). The reactivity of RA serum IgG antibodies against K8 was significantly higher than healthy controls and systemic lupus erythematosus (SLE) patients. CONCLUSION: This research confirmed Keratin 8 as a novel autoantigen of RA.

Prohibitin as a novel autoantigen in rheumatoid arthritis.

THE AIM OF THIS STUDY: The aim of this study was to verify whether prohibitin is a novel autoantigen in rheumatoid arthritis. MATERIAL AND METHODS: First, recombinant human prohibitin (rhPHB) protein was cloned, expressed, and purified. Then the anti-prohibitin autoantibodies were detected by western blotting by using rhPHB protein to incubate sera from patients with rheumatoid arthritis (RA). Next, immunoprecipitation was employed to further illustrate whether anti-prohibitin antibodies exist in RA patients. And finally, autoantibodies against the rhPHB protein were investigated using a homemade ELISA kit through the assessment of 258 real clinical samples. RESULTS: It was revealed that anti-prohibitin antibodies existed in the sera of patients with RA. Reactivity of serum IgG against rhPHB was detected in 26 of 86 RA patients (30.3%), 7 of 86 systemic lupus erythematosus (SLE) patients (8.1%), and 1 of 86 apparently healthy donors (HC) (1.2%). CONCLUSIONS: Prohibitin was proved to be a novel autoantigen and the corresponding anti-prohibitin autoantibodies were present in the RA patients' blood circulation.

Multiple correlations of mRNA expression and protein abundance in human cytokine profile.

With the development of genomic study, researchers found that it is insufficient to predict protein expression from quantitative mRNA data in large scale, which is contrary to the traditional opinion that mRNA expression correlates with protein abundance at the single gene level. To try to solve the apparent conflicting views, here we set up a series of research models and chose soluble cytokines as targets. First, human peripheral blood mononuclear cell (PBMC) from one health donor was treated with 16 continuously changing conditions, the protein and mRNA profile were analyzed by multiplex Luminex and genomic microarray, respectively. Among the tested genes, around half mRNA correlated well with their corresponding proteins (ρ > 0.8), however if we put all the genes together, the correlation coefficient for the 16 conditions varied from 0.29 to 0.71. Second, PBMC from 14 healthy donors were stimulated with the same condition and it was found that the correlation coefficient went down (ρ < 0.6). Third, 28 rheumatoid arthritis (RA) patients were tested for their response to the same external stimuli and it turned out different individual displayed different protein expression pattern as expect. Lastly, autoimmune disease cohorts (8 diseases including RA, 103 patients in total) were assayed on the whole view. It was observed that there was still some similarity in the protein profile among patients from the single disease type although completely different patterns were displayed across different disease categories. This study built a good bridge between single gene analysis and the whole genome study and may give a reasonable explanation for the two conflicting views in current biological science.

[Clinical features and risk factors of co-morbid tic disorder in children with attention deficit hyperactivity disorder].

OBJECTIVE: To study the clinical features and risk factors of co-morbid tic disorder (TD) in children with attention deficit hyperactivity disorder (ADHD). METHODS: A total of 312 children with ADHD were involved in this study. Subtypes of co-morbid TD, incidences of TD in different subtypes of ADHD (ADHD-I, ADHD-HI and ADHD-C) were observed. Thirteen potential factors influencing the comorbidity rate of TD in ADHD were evaluated by univariate analysis and multiple logistic regression analysis. RESULTS: Forty-two of 312 children with ADHD suffered from co-morbid TD (13.5%). Comorbidity rate of TD in children with ADHD-C (24.1%) was significantly higher than in those with ADHD-HI (10.9%) and ADHD-I (8.8%) (P<0.05). There were 21 cases (50.0%) of transient TD, 12 cases (28.6%) of chronic TD, and 9 cases (21.4%) of Tourette syndrome. The univariate analysis revealed 6 factors associated with comorbidity: addiction to mobile phone or computer games, poor eating habits, infection, improper family education, poor relationship between parents and poor relationship with schoolmates. Multiple logistic analysis revealed two independent risk factors for comorbidity: improper family education (OR=7.000, P<0.05) and infection (OR=2.564, P<0.05). CONCLUSIONS: The incidence of co-morbid TD in children with ADHD is influenced by many factors, and early interventions should be performed based on the main risk factors.

Disposal of drilling waste in salt mines in China.

A lot of drilling wastes are produced during oil/gas exploration and exploitation in China. Many countries have built and successfully run projects to dispose of wastes in salt mines, which fully demonstrates the feasibility and superiority of this technology. The application prospects of using salt mines to dispose of drilling wastes is comprehensively evaluated from many aspects. It is concluded that this technology has broad application prospects in China. The scientific and technical problems that need to be solved in order to successfully use this technology are systematically summarized, and some practical suggestions are put forward to improve relevant laws and policies. Considering the geological conditions of salt mines and the requirements of laws and regulations in China, a set of perfect and more advanced Chinese schemes has been proposed.

AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System.

Genome editing is the basis for the modification of engineered microbes. In the process of genome editing, the design of editing sequences, such as primers and sgRNA, is very important for the accurate positioning of editing sites and efficient sequence editing. The whole process of genome editing involves multiple rounds and types of editing sequence design, while the development of related whole-workflow design tools for high-throughput experimental requirements lags. Here, we propose AutoESDCas, an online tool for the end-to-end editing sequence design for microbial genome editing based on the CRISPR/Cas system. This tool facilitates all types of genetic manipulation covering diverse experimental requirements and design scenarios, enables biologists to quickly and efficiently obtain all editing sequences needed for the entire genome editing process, and empowers high-throughput strain modification. Notably, with its off-target risk assessment function for editing sequences, the usability of the design results is significantly improved. AutoESDCas is freely available at https://autoesdcas.biodesign.ac.cn/with the source code at https://github.com/tibbdc/AutoESDCas/.

Age-Related Variations in the Population of Active Secondary Hair Follicles, Oxidative Stress and Antioxidant Parameters in Cashmere Goats.

The objective of this study was to investigate age-related changes in cashmere production and the population of active secondary hair follicles in cashmere goats across different age groups as well as to explore the association between secondary hair follicle activity and oxidative stress. A total of 104 adult Inner Mongolian ewe goats, aged between 2 and 7 years old, were randomly selected as experimental subjects. Skin samples were collected in August 2020 and cashmere samples were collected in April 2021. The cashmere fiber yield, staple length, and diameter showed age-related variations in cashmere goats aged 2 to 7 years (p < 0.05). Cashmere production was higher in goats aged 2-4 years compared to those aged 5-7 years (p < 0.05). There were no significant differences in the population of primary and secondary hair follicles among goats aged 2 to 7 years. However, the population of active secondary hair follicles varied significantly with age, with the younger group (aged 2-4 years) having a higher population than those aged 5-7 years (p < 0.05). A moderate negative correlation was observed between cashmere fiber diameter and the population of active secondary hair follicles (p < 0.05). Age-related variations in skin antioxidant capacity and oxidative damage were observed among cashmere goats aged 2 to 7 years old (p < 0.05). Goats aged 2 to 4 years exhibited higher antioxidant capacity and lower oxidative damage (p < 0.05). Interestingly, the skin's antioxidant capacity and oxidative damage exhibited significant positive and negative correlations with the population of active secondary hair follicles (p < 0.05). This study presents a novel approach to enhance the activity of secondary hair follicles and improve cashmere production performance through the regulation of oxidative stress.

Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli.

Utilizing standardized artificial regulatory sequences to fine-tuning the expression of multiple metabolic pathways/genes is a key strategy in the creation of efficient microbial cell factories. However, when regulatory sequence expression strengths are characterized using only a few reporter genes, they may not be applicable across diverse genes. This introduces great uncertainty into the precise regulation of multiple genes at multiple expression levels. To address this, our study adopted a fluorescent protein fusion strategy for a more accurate assessment of target protein expression levels. We combined 41 commonly-used metabolic genes with 15 regulatory sequences, yielding an expression dataset encompassing 520 unique combinations. This dataset highlighted substantial variation in protein expression level under identical regulatory sequences, with relative expression levels ranging from 2.8 to 176-fold. It also demonstrated that improving the strength of regulatory sequences does not necessarily lead to significant improvements in the expression levels of target proteins. Utilizing this dataset, we have developed various machine learning models and discovered that the integration of promoter regions, ribosome binding sites, and coding sequences significantly improves the accuracy of predicting protein expression levels, with a Spearman correlation coefficient of 0.72, where the promoter sequence exerts a predominant influence. Our study aims not only to provide a detailed guide for fine-tuning gene expression in the metabolic engineering of Escherichia coli but also to deepen our understanding of the compatibility issues between regulatory sequences and target genes.

Facile one-step synthesis and transformation of Cu(I)-doped zinc sulfide nanocrystals to Cu(1.94)S-ZnS heterostructured nanocrystals.

A facile one-pot heating process without any injection has been developed to synthesize different Cu-Zn-S-based nanocrystals. The composition of the products evolves from Cu(I)-doped ZnS (ZnS:Cu(I)) nanocrystals into heterostructured nanocrystals consisting of monoclinic Cu1.94S and wurtzite ZnS just by controlling the molar ratios of zinc acetylacetonate (Zn(acac)2) to copper acetylacetonate (Cu(acac)2) in the mixture of n-dodecanethiol (DDT) and 1-octadecene (ODE). Accompanying the composition transformation, the crystal phase of ZnS is changed from cubic zinc blende to hexagonal wurtzite. Depending on the synthetic parameters including the reaction time, temperature, and the feeding ratios of Zn/Cu precursors, the morphology of the as-obtained heterostructured nanocrystals can be controlled in the forms of taper-like, matchstick-like, tadpole-like, or rod-like. Interestingly, when the molar ratio of Cu(acac)2 to Zn(acac)2 is increased to 9:1, the crystal phase of the products is transformed from monoclinic Cu1.94S to the mixed phase composed of cubic Cu1.8S and tetragonal Cu1.81S as the reaction time is further prolonged. The crystal-phase transformation results in the morphological change from quasi-spherical to rice shape due to the incorporation of Zn ions into the Cu1.94S matrix. This method provides a simple but highly reproducible approach for synthesis of Cu(I)-doped nanocrystals and heterostructured nanocrystals, which are potentially useful in the fabrication of optoelectronic devices.

Controllable synthesis of silver and silver sulfide nanocrystals via selective cleavage of chemical bonds.

A one-step colloidal process has been adopted to prepare silver (Ag) and silver sulfide (Ag2S) nanocrystals, thus avoiding presynthesis of an organometallic precursor and the injection of a toxic phosphine agent. During the reaction, a layered intermediate compound is first formed, which then acts as a precursor, decomposing into the nanocrystals. The composition of the as-obtained products can be controlled by selective cleavage of S-C bonds or Ag-S bonds. Pure Ag2S nanocrystals can be obtained by directly heating silver acetate (Ag(OAc)) and n-dodecanethiol (DDT) at 200 ° C without any surfactant, and pure Ag nanocrystals can be synthesized successfully if the reaction temperature is reduced to 190 ° C and the amount of DDT is decreased to 1 ml in the presence of a non-coordinating organic solvent (1-octadecene, ODE). Otherwise, the mixture of Ag and Ag2S is obtained by directly heating Ag(OAc) in DDT by increasing the reaction temperature or in a mixture of DDT and ODE at 200 ° C. The formation mechanism has been discussed in detail in terms of selective S-C and Ag-S bond dissociation due to the nucleophilic attack of DDT and the lower bonding energy of Ag-S. Interestingly, some products can easily self-assemble into two- or three-dimensional (2D or 3D) highly ordered superlattice structures on a copper grid without any additional steps. The excess DDT plays a key role in the superlattice structure due to the bundling and interdigitation of the thiolate molecules adsorbed on the as-obtained nanocrystals.