Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast.

Performing saturation editing of chromosomal genes will enable the study of genetic variants in situ and facilitate protein and cell engineering. However, current in vivo editing of endogenous genes either lacks flexibility or is limited to discrete codons and short gene fragments, preventing a comprehensive exploration of genotype-phenotype relationships. To enable facile saturation editing of full-length genes, we used a protospacer adjacent motif-relaxed Cas9 variant and homology-directed repair to achieve above 60% user-defined codon replacement efficiencies in Saccharomyces cerevisiae genome. Coupled with massively parallel DNA design and synthesis, we developed a saturation gene editing method termed CRISPR-Cas9- and homology-directed repair-assisted saturation editing (CHASE) and achieved highly saturated codon swapping of long genomic regions. By applying CHASE to massively edit a well-studied global transcription factor gene, we found known and unreported genetic variants affecting an industrially relevant microbial trait. The user-defined codon editing capability and wide targeting windows of CHASE substantially expand the scope of saturation gene editing.

Discovery of ß-sitosterol's effects on molecular changes in rat diabetic wounds and its impact on angiogenesis and macrophages.

Diabetes care, particularly for diabetic foot ulcers (DFUs)-related complications, increases treatment costs substantially. Failure to provide timely and appropriate treatment for severe DFUs significantly increases amputation risk. Neovascularization and macrophage polarization play an important role in diabetic wound healing during different stages of the wound repair process. Therefore, a new treatment method that promotes neovascularization and macrophage polarization may accelerate diabetic wound healing. ß-sitosterol possesses anti-inflammatory, lipid-lowering, and antidiabetic properties. However, its therapeutic potential in diabetic wound healing remains underexplored. This study evaluated the healing effects of ß-sitosterol on diabetic ulcer wounds in rats. We found that ß-sitosterol can promote angiogenesis, alternatively activated macrophages (M2 macrophage) proliferation, and collagen synthesis in diabetic wounds. Transcriptomics analysis and proteomics analysis revealed that MAPK, mTOR and VEGF signaling pathways were enriched in ß-sitosterol-treated wounds. Molecular docking revealed Ndufb5 maybe the target of ß-sitosterol-treated wounds. Our findings confirm the significant diabetic wound healing effects of ß-sitosterol in a rat model. ß-sitosterol treatment to diabetic wounds accelerates wound healing through promoting M2 macrophage proliferation and angiogenesis. Interestingly, we also found that the process of M2 macrophage proliferation accompanies angiogenesis. Thus, ß-sitosterol may be a promising therapeutic approach to enhance diabetic wound healing and reduce amputation in diabetes.

Polymer-in-Salt Electrolyte from Poly(caprolactone)-graft-polyrotaxane for Ni-Rich Lithium Metal Batteries at Room Temperature.

Solid-state lithium batteries with solid polymer electrolytes have recently attracted extensive attention due to their promising potential in high energy density and safety. However, the principal issues plaguing the solid polymer electrolytes are their restricted ionic conductivities at ambient temperature and the limited tolerance to the widely used high-voltage cathodes (such as LiNi0.8Mn0.1Co0.1O2, NCM811), thus limiting their practical applications seriously. In this regard, a superior polymer-in-salt solid electrolyte from poly(caprolactone)-graft-polyrotaxane (PGPE) is developed for high-voltage lithium batteries operated at room temperature. The PGPE displays remarkable electrochemical properties at room temperature, with an exceptional ionic conductivity of 4.89 × 10-4 S cm-1 and a lithium-ion transference number of approximately 0.64, stemming from the rapid segmental motions of PCL sidechains by the enhanced dynamics of the cyclic molecules along the axial polymer chain of polyrotaxane. More importantly, the PGPE demonstrates a high electrochemical oxidation voltage of ∼4.7 V, suggesting the excellent electrochemical stability of PGPE against the NCM811-based cathode. Owing to the dense LiF-rich CEI self-generated on the NCM811 particles in the cathode, the transition metal ion diffusion is successfully constrained and the PGPE is well protected from continuous decomposition. The PGPE also shows superior interfacial stability between the metallic Li and the electrolyte. As a result, the all-solid-state NCM811|PGPE|Li cell exhibits superior discharge capacity (196 mAh g-1) and extraordinary long-term cycling stability (74% capacity retention at 150 cycles) at 30 °C.

Super-Branched PdCu Alloy for Efficiently Converting Carbon Dioxide to Carbon Monoxide.

The alloying of noble metals with Cu is one of the most effective strategies for improving catalytic performance and reducing cost in electrocatalytic carbon dioxide reduction reactions (CO2RR). Previous works usually focused on the influence of morphology and composition on the catalytic activity, but lacked the study of the valence state ratio of metals and the electron transfer behavior on alloys. In this work, PdCu-2 alloy (Pd/Cu molar ratio is 1:2) was obtained by a simple one-step solvothermal method, which can effectively convert CO2 to CO with a maximum Faradaic efficiency (FE) of 85% at -0.9 V (vs. RHE). Then, the effect of the chemical state of Pd and Cu on the catalytic performance was investigated. The X-ray photoelectron spectroscopy (XPS) shows that the binding energy of Pd in PdCu alloy has a negative shift, which has affected the adsorption of key intermediates. When the proportion of oxidized state and zero-valent metal in the alloy is about 1:2, the PdCu alloy shows the best catalytic activity. In addition, the transient photovoltage (TPV) measurements further demonstrate that due to the introduction of Cu, the electron transfer rate of PdCu-2 becomes the slowest, which helps the accumulation of electrons on PdCu-2 and leads to the improvement of catalytic performance for electrocatalytic CO2RR. This work can provide more insights into the alloy catalysts of electrocatalytic CO2RR.

Native and engineered extracellular vesicles for wound healing.

Extracellular vesicles (EVs) that act as messengers mediate communication between parent and recipient cells through their contents, including nucleic acids, proteins, and lipids. These endogenous vesicles have emerged as a novel cell-free strategy for the treatment of diseases. EVs can be released by various types of cells with unique biological properties. Recent studies have shown that native EVs are used as therapeutic agents to promote tissue repair by delivering various growth factors and trophic factors including VEGF, EGF, TFN-α, IL-1ß, and TGF-ß to participate in all physiological processes of wound healing. Furthermore, to improve their specificity, safety, and efficiency for wound healing, the content and surface of EVs can be designed, modified, and engineered. The engineering strategies of EVs are divided into parent cell modification and indirect modification of EVs. The therapeutic potential of current EVs and engineered EVs for wound healing still requires the exploration of their large-scale clinical applications through innovative approaches. Herein, we provide an overview of the current biological knowledge about wound healing and EVs, as well as the application of native EVs in promoting wound healing. We also outline recent advances in engineering EV methodologies to achieve ideal therapeutic potential. Finally, the therapeutic applications of engineered EVs in wound healing are reviewed, and the challenges and prospects for the translation of engineered EVs to clinical applications are discussed.

Intra-Articular Biomechanical Changes of the Meniscus and Ligaments During Stance Phase of Gait Circle after Different Anterior Cruciate Ligament Reconstruction Surgical Procedures: A Finite Element Analysis.

OBJECTIVE: The debate on the superiority of single- or double-bundle for anterior cruciate ligament reconstruction has not ceased. The comparative studies on intra-articular biomechanics after different surgical reconstructions are rare. This study is to evaluate the biomechanical stress distribution intra-knee after single- and double-bundle anterior cruciate ligament reconstruction by three-dimensional finite element analysis, and to observe the change of stress concentration under the condition of vertical gradient loads. METHODS: In this study, magnetic resonance imaging data were extracted from patients and healthy controls for biomechanical analysis. Patients included in the three models were matched in age and sex. The strength and distribution of induced stresses were analyzed in two frequently used procedures, anatomical single-bundle anterior cruciate ligament reconstruction and anatomical double-bundle anterior cruciate ligament reconstruction, using femoral-graft-tibial system under different loads, to mimic a post-operation mechanical motion. The three-dimensional finite-element models for normal ligament and two surgical methods were applied. A vertical force simulating daily walking was performed on the models to assess the interfacial stresses and displacements of intra-articular tissues and ligaments. The evaluation results mainly included the stress of each part of ligament and meniscus. The stress values of different parts of three models were extracted and compared. RESULTS: The stress of ligament/graft at femoral side of three finite-element models was significantly higher than at tibial side, while the highest level was observed in single-bundle reconstruction finite-element model. With the increase of force, the maximum stress in the medial (7.1-7.1 MPa) and lateral (4.9-7.4 MPa) meniscus of single-bundle reconstruction finite-element model shifted from the anterior horn to the central area (p = 0.0161, 0.0479, respectively). The stress was shown to be at a lower level at femoral side and posterior cruciate ligament of intra-knee in two reconstruction finite-element models than that in normal finite-element models, while presented higher level at the tibial side than normal knee (p = 0.3528). The displacement of the femoral side and intra-knee areas in reconstruction finite-element models was greater than that in normal finite-element model (p = 0.0855). CONCLUSION: Compared with the single-bundle technique, the graft of double-bundle anterior cruciate ligament reconstruction has better stress dissipation effect and can prevent postoperative meniscus tear more effectively.

NR2F1-AS1/miR-190a/PHLDB2 Induces the Epithelial-Mesenchymal Transformation Process in Gastric Cancer by Promoting Phosphorylation of AKT3.

The median survival time of patients with advanced gastric cancer (GC) who received radiotherapy and chemotherapy was <1 year. Epithelial-mesenchymal transformation (EMT) gives GC cells the ability to invade, which is an essential biological mechanism in the progression of GC. The long non-coding RNA (lncRNA)-based competitive endogenous RNA (ceRNA) system has been shown to play a key role in the GC-related EMT process. Although the AKT pathway is essential for EMT in GC, the relationship between AKT3 subtypes and EMT in GC is unclear. Here, we evaluated the underlying mechanism of ceRNA involving NR2F1-AS1/miR-190a/PHLDB2 in inducing EMT by promoting the expression and phosphorylation of AKT3. The results of bioinformatics analysis showed that the expression of NR2F1-AS1/miR-190a/PHLDB2 in GC was positively associated with the pathological features, staging, poor prognosis, and EMT process. We performed cell transfection, qRT-PCR, western blot, cell viability assay, TUNEL assay, Transwell assay, cell morphology observation, and double luciferase assay to confirm the regulation of NR2F1-AS1/miR-190a/PHLDB2 and its effect on EMT transformation. Finally, GSEA and GO/KEGG enrichment analysis identified that PI3K/AKT pathway was positively correlated to NR2F1-AS1/miR-190a/PHLDB2 expression. AKT3 knockout cells were co-transfected with PHLDB2-OE, and the findings revealed that AKT3 expression and phosphorylation were essential for the PHLDB2-mediated EMT process. Thus, our results showed that NR2F1-AS1/miR-190a/PHLDB2 promoted the phosphorylation of AKT3 to induce EMT in GC cells. This study provides a comprehensive understanding of the underlying mechanism involved in the EMT process as well as the identification of new EMT markers.

Anaerobic co-digestion of textile dyeing sludge: Digestion efficiency and heavy metal stability.

Anaerobic co-digestion (AcoD) has become an important mean for the stabilization and recycling of textile dyeing sludge (TDS). Using the soybean okara byproduct (SOB) as a co-digestion substrate, the effects on AcoD performance and heavy metal stability were studied. The results indicated that the optimal mixing ratio was 1:1 (calculated by total sloid). Under this condition, the SCOD removal efficiency was 64% (that of TDS alone and SOB alone were 47% and 48%, respectively) and the cumulative methane production field was 503 L CH4/kg VS (that of TDS alone and SOB alone were 435 L CH4/kg VS and 408 L CH4/kg VS, respectively). At the same time, the addition of SOB could also enhance the stability of heavy metals (Zn, Cu, Cr and Ni) in TDS. Remarkably, that could increase the steady state content nickel from 47.98% to 57.21%, while anaerobic digestion of TDS caused no increase but a decrease (only 42.13%). According to the risk assessment code analyses, the AcoD of TDS by SOB can significantly reduce the ecotoxicity risk caused by Ni, Zn and Cr.

Differential Expression Profiles and Function Predictions for tRFs & tiRNAs in Skin Injury Induced by Ultraviolet Irradiation.

Ultraviolet (UV) radiation is a major environmental factor contributing skin damage. As UV exposure is inevitable, it is necessary to pay attention to the underlying molecular mechanisms of UV-induced skin damage to develop effective therapies. tRNA-derived stress-induced RNAs (tiRNAs) and tRNA-derived fragments (tRFs) are tRNA-derived small RNAs (tsRNAs) that are a novel class of short, non-coding RNAs. However, the functions behind tRFs & tiRNAs in UV-induced skin injury are not yet clear. Firstly, the animal model of ultraviolet irradiation induced skin damage was established. Then the skin samples were preserved for the follow-up experiment. Sequencing was used to screen expression profiles and predict target genes. Compared with normal skin, a total of 31 differentially expressed tRFs & tiRNAs were screened. Among these, 10 tRFs & tiRNAs were shown to be significantly different in expression levels, where there were 4 up-regulated and 6 down-regulated target genes. Bioinformatics analyses revealed potential up-regulated tsRNAs (tRF-Val-AAC-012, tRF-Pro-AGG-012, tRF-Val-CAC-018, tRF-Val-AAC-031) and down-regulated tsRNAs (tRF-Arg-CCT-002, tRF-Trp-TCA-001, tiRNA-Ser-GCT-001, tRF-Gly-CCC-019, tRF-Ala-TGC-001, tRF-Ala-TGC-002). In summary, it was speculated that tRF-Gly-CCC-019 plays an important role in acute skin injury induced by UVB radiation by regulating the ras-related C3 botulinum toxin substrate 1 (Rac1) gene in the WNT signaling pathway. This study provides new insights into the mechanisms and therapeutic targets of UV-induced skin injury.

Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.

An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.

Development and Validation of a Prognostic Nomogram for Gastric Signet Ring Cell Carcinoma: A Multicenter Population-Based Study.

BACKGROUND: Gastric signet ring cell carcinoma (GSRCC) is a rare disease associated with poor prognosis. A prognostic nomogram was developed and validated in this study to assess GSRCC patients' overall survival (OS). METHODS: Patients diagnosed with GSRCC from the Surveillance, Epidemiology, and End Results (SEER) database (2004-2016) and the First Hospital of China Medical University (CMU1h) were enrolled in this retrospective cohort study. Univariate and multivariate COX analysis was used to determine independent prognostic factors to construct the prognostic nomogram. Predictions were evaluated by the C-index and calibration curve. In addition, the receiver operating characteristic (ROC) curve, decision curve analysis (DCA), and Kaplan-Meier analysis were employed to assess the clinical utility of the survival prediction model. RESULTS: Patients were classified into two cohorts. We randomly divided patients in the SEER database and CMU1h cohort into a training group (n=3068, 80%) and a validation group (n=764, 20%). Age, race, T stage, N stage, M stage, therapy, and tumor size were significantly associated with the prognosis of GSRCC patients. On this basis, a nomogram was constructed, with a C-index in the training and the validation cohorts at 0.772 (95% CI: 0.762-0.782) and 0.774 (95% CI: 0.752-0.796), respectively. The accuracy of the generated nomogram was verified through calibration plots. Similarly, compared with the traditional AJCC staging system, the results of the area under curve (AUC) calculated by ROC, DCA, and Kaplan-Meier curves, demonstrated a good predictive value of the constructed nomogram, compared to the traditional AJCC staging system. CONCLUSION: In the present study, seven independent prognostic factors of GSRCC were screened out. The established nomogram models based on seven variables provided a visualization of each prognostic factor's risk and assisted clinicians in predicting the 1-, 3-, and 5-year OS of GSRCC.

Comparison of efficacy between natural orifice specimen extraction without abdominal incision and conventional laparoscopic surgery in the treatment of sigmoid colon cancer and upper rectal cancer.

PURPOSE: To compare the short-term efficacy between natural orifice specimen extraction (NOSE) without abdominal incision and conventional laparoscopic surgery in the treatment of sigmoid colon cancer and upper rectal cancer. METHODS: A total of 86 patients scheduled to undergo laparoscope-assisted radical surgery of sigmoid cancer or upper rectal cancer from January 2015 to September 2017 (T1-3 stages in preoperative imaging evaluation, no distant metastasis, and body mass index <28 kg/m2) were selected and randomly divided into the NOSE group (no abdominal incision, n=43) and conventional laparoscopy group (LA group, n=43). The operation time, amount of intraoperative bleeding, postoperative exhaust time, postoperative diet time, postoperative hospitalization duration, postoperative pain score and perioperative complications were compared between the two groups. The pathological conditions of surgical specimens were recorded. The postoperative recurrence rate of tumor and survival rate of patients were also recorded and compared. RESULTS: The general clinical features were comparable between the two groups, and there were no perioperative deaths. The operation time in NOSE group was slightly longer than that in LA group, without statistically significant difference (p=0.130). In NOSE group, the amount of intraoperative bleeding was significantly smaller than in LA group [(59.31±14.64) mL vs. (75.41±18.16) mL, p<0.001], the postoperative visual analogue scale (VAS) score was significantly lower than that in LA group [(4.2±1.6) points vs. (5.9±1.4) points, p<0.001], and the postoperative exhaust time and regular diet time were significantly shorter than those in LA group [(2.1±1.0) d vs. (2.6±1.2) d, p=0.039, (3.8±1.1) d vs. (4.4±1.4) d, p=0.030]. The cosmetic result in NOSE group was better than that in LA group [(8.0±1.5) vs. (6.4±1.1), p<0.001]. Moreover, the comparison results of surgical specimens showed that there were no statistically significant differences in the intestine resection length, proximal and distal resection margins, tumor size, number of lymph nodes dissected and TNM stage of tumor between the two groups (p>0.05). The postoperative tumor recurrence rate had no significant difference between the two groups (p=0.359), and the Log-rank test revealed that the disease-free survival (DFS) rate had no statistically significant difference between the two groups (p=0.280). CONCLUSIONS: NOSE without abdominal incision has a comparable short-term clinical efficacy to conventional laparoscopic surgery in the treatment of sigmoid cancer and upper rectal cancer, but it significantly reduces the amount of intraoperative bleeding and lowers the pain of patients, with rapid postoperative recovery and high safety, so it is worthy of clinical popularization.

Effects of degree of carboxymethylation on physicochemical and biological properties of pachyman.

Polysaccharides (pachyman) extracted from Poria cocos sclerotium were chemically modified by carboxymethylation and the effects on the structural and biological properties of the polysaccharides were investigated as a function of the degree of carboxymethylation. The degree of substitution (DS) of five carboxymethylated pachyman, coded as CMP1/CMP2/CMP3/CMP4/CMP5, was determined to be 0.44-0.88. The structures were confirmed by FT-IR and their weight-average molecular masses (Mw) were obtained by SEC-LLS. Experimental results showed that derivatives were effective in anti-oxidation and bile acid binding in a dose dependent way. Furthermore, their water solubility and biological activities were improved with the increase of DS. Therefore, results proved that the carboxymethylation of pachyman effectively enhanced their potential biological properties.