Synthetic biology is an emerging interdisciplinary field at the convergence of biology, engineering, and computer science. It employs a bottom-up approach to progressively design biological parts, devices, and circuits, aiming to create artificial biological systems not found in nature or to redesign existing biological systems for specific purposes. With the rapid development of the synthetic biology industry, there is an increasing demand for large complex genetic circuits. However, the traditional trial-and-error methods, heavily reliant on empirical knowledge, have limited efficiency and success rates of parts/circuits construction, thereby impeding the innovation and technology translation for synthetic biology. These limitations have prompted a paradigm shift from labor-intensive, experience-driven trial-and-error models towards standardized, intelligent engineering approaches. Machine learning, capable of uncovering hidden structures and relationships within biological data, offers robust support for the intelligent design of synthetic biological parts and genetic circuits. Here, we review commonly used machine learning algorithms and analyze their typical applications in designing biological parts (e.g., synthetic promoters, RNA regulatory elements, and transcription factors) and simple genetic circuits. Additionally, we discuss the primary challenges in machine learning-aided design and propose potential solutions. Lastly, we envision the future trend of integrating machine learning with synthetic biological system design, highlighting the importance of interdisciplinary collaboration.
Synthetic Biology/methods* ; Machine Learning ; Gene Regulatory Networks ; Algorithms

Malignant pleural effusion(MPE)is a common complication in patients with advanced malignant tumors,which not only significantly reduces their quality of life but also shortens their survival duration.Despite the widespread use of traditional treatment methods such as thoracentesis and pleurodesis,their efficacy is limited accompanied by high recurrence rates.Therefore,exploring novel therapeutic strategies becomes particularly urgent.In recent years,immunotherapy has attracted extensive attention for its potential in cancer treatment.This article systematically reviews the roles of CD4+T cell subsets,including regulatory T cells(Treg),T helper cell(Th)17,Th9,and Th22 cells,within the immunosuppressive microenvironment of MPE.These cell subsets are involved in the formation of the immunosuppressive state of MPE through various mechanisms and play key roles in the occurrence and development of the disease.In addition,the article discusses in detail the role of immune checkpoint molecules,such as programmed death protein 1(PD-1),PD-1 ligand(PD-L1),and cytotoxic T-lymphocyte-associated protein 4(CTLA-4),in the immune evasion of MPE.The abnormal expressions of these molecules provide opportunity for tumor cells to evade immune system surveillance.At the same time,this article also summarizes the application prospects of novel immunotherapy strategies,such as adoptive cell therapy(ACT)and chimeric antigen receptor T cell(CAR-T)therapy,in the treatment of MPE.These innovative therapies offer possibilities for improving the prognosis of MPE patients through activating and enhancing the anti-tumor immune response.

Objective:To investigate the effects of fluoride exposure on kidney injury in rats and the sirtuin 3 (SIRT3)-fork head protein O3a (FOXO3a)-tensin homolog induced putative kinase 1 (PINK1)/E3 ubiquitin ligase (PARKIN) pathway.Methods:Twenty-four 4-week-old SD rats (clean grade, body mass 100 - 150 g) were selected and divided into three groups according to the randomized numeric table: control group, low fluoride group, and high fluoride group, with eight rats in each group (half male and half female). The control group was given free access to tap water (fluoride ion concentration < 0.5 mg/L), while the low fluoride and high fluoride groups were given free access to tap water and sodium fluoride solutions with fluoride ion concentrations of 5.0 and 50.0 mg/L, respectively, for a period of 180 days. The formation of dental fluorosis in rats was observed and recorded, and the femur, urine and blood samples of rats were collected to measure bone fluoride, urinary fluoride, and blood fluoride levels, and to detect kidney function related indicators (serum uric acid, creatinine, and urea nitrogen contents). Morphological changes of renal tissues stained with hematoxylin-eosin (HE) were observed under a light microscope. Real-time fluorescence quantitative PCR (qRT-PCR) and Western blotting were used to detect the mRNA and protein expression levels of renal SIRT3, FOXO3a, PINK1, PARKIN, microtubule associated protein 1 light chain 3 (LC3), autophagy receptor protein (P62), respectively.Results:Seven and one rats in the low and high fluoride groups were found to haveⅠdegree dental fluorosis, while zero and seven rats were found to haveⅡdegree dental fluorosis. Compared with the control group, rats in the low and high fluoride groups had higher levels of bone fluoride (μg/g: 1.18 ± 0.06, 2.16 ± 0.07 vs 0.52 ± 0.05), urinary fluoride (mg/L: 4.43 ± 0.11, 7.46 ± 0.09 vs 2.58 ± 0.14), blood fluoride (μg/ml: 0.77 ± 0.06, 1.68 ± 0.10 vs 0.52 ± 0.08), serum uric acid (μg/ml: 61.01 ± 4.17, 103.92 ± 5.43 vs 28.68 ± 2.91), creatinine (μg/ml: 74.82 ± 9.61, 132.05 ± 5.35 vs 22.38 ± 4.11), and urea nitrogen (μg/ml: 13.36 ± 1.27, 14.55 ± 0.34 vs 0.29 ± 0.07, P < 0.05). Under the light microscope, the kidneys of the control group showed tight and orderly arrangement of renal tubules and glomerular cells, with complete and clear cell contours. The low fluoride group was similar to the control group and no significant abnormalities were observed. The high fluoride group showed abnormal glomerular structure and atrophy, with some areas of renal tubules showing epithelial cell edema and unclear intercellular boundaries. The results of qRT-PCR assay showed that compared with the control group, the low and high fluoride groups had lower mRNA expression levels of SIRT3 (0.82 ± 0.03, 0.58 ± 0.02 vs 1.00 ± 0.08), P62 (0.75 ± 0.07, 0.28 ± 0.09 vs 1.00 ± 0.07, P < 0.05), and higher mRNA expression levels of FOXO3a (1.35 ± 0.04, 3.01 ± 0.23 vs 1.00 ± 0.08), PINK1 (1.58 ± 0.09, 3.28 ± 0.09 vs 1.00 ± 0.07), PARKIN (1.51 ± 0.04, 1.67 ± 0.10 vs 1.00 ± 0.05), LC3 (1.74 ± 0.07, 2.38 ± 0.18 vs 1.00 ± 0.08, P < 0.05). The results of Western blotting showed that compared with the control group, the low and high fluoride groups had lower protein expression levels of SIRT3 (0.91 ± 0.01, 0.55 ± 0.03 vs 1.00 ± 0.01), P62 (0.94 ± 0.27, 0.66 ± 0.38 vs 1.00 ± 0.19, P < 0.05), and higher protein expression levels of FOXO3a (1.14 ± 0.03, 1.22 ± 0.05 vs 1.00 ± 0.02), PINK1 (1.46 ± 0.03, 1.56 ± 0.03 vs 1.00 ± 0.05), PARKIN (1.98 ± 0.02, 2.33 ± 0.11 vs 1.00 ± 0.06), LC3 (4.10 ± 0.58, 4.93 ± 0.33 vs 1.00 ± 0.13, P < 0.05). Conclusion:Exposure to fluoride can cause renal tissue injury in rats, with downregulation of SIRT3 and P62 expression levels, and upregulation of FOXO3a, PINK1, PARKIN, and LC3 expression levels.

ObjectiveTo screen out the transcriptomes related to the intervention of Wuzi Yanzongwan on the spermatogenic function of semi-castrated male mice， and to explore its potential mechanism in the intervention of the progress of low spermatogenic function. MethodBalb/c mice were randomly divided into sham-operated group， model group， testosterone propionate group（0.2 mg·kg^-1·d^-1， intramuscular injection） and Wuzi Yanzongwan group（1.56 g·kg^-1·d^-1， intragastric administration） according to body weight， with 12 mice in each group. The right testicle and epididymis were extracted from the model group and the drug administration group to construct the semi-castrated model of low spermatogenic function， while the fur and the right scrotum of the sham-operated group were only cut and immediately sterilized and sutured. At the end of the intervention， hematoxylin-eosin（HE） staining was used to observe the histopathology of testis， enzyme-linked immunosorbent assay（ELISA） was used to detect the levels of serum testosterone（T）， luteinizing hormone（LH） and follicle stimulating hormone（FSH）. The sperm count and motility of epididymis were measured by automatic sperm detector of small animal. Transcriptomic microarray technology was used to detect the mRNA expression level of testicular tissue in each group， the transcriptome of genes related to the regulation of Wuzi Yanzongwan was screened， and three mRNAs were selected for Real-time fluorescence quantitative polymerase chain reaction（Real-time PCR） to verify the transcriptome data. Through the annotation analysis of Gene Ontology（GO） and the signaling pathway analysis of Kyoto Encyclopedia of Genes and Genomes（KEGG）， the related functions of drugs regulating transcriptome were analyzed. ResultCompared with the sham-operated group， the testicular tissue of mice in the model group showed spermatogenic injury， contraction and vacuolization of the seminiferous tubules， reduction of spermatogenic cells at all levels， widening of the interstitial space， obstruction of spermatogonial cell development and other morphological abnormalities， and serum T significantly decreased， LH significantly increased（P<0.01）， and FSH elevated but no statistically significant difference， the count and vitality of epididymal sperm significantly decreased（P<0.01）. There were 882 differentially expressed mRNAs in the testicular tissues， of which 565 were up-regulated and 317 were down-regulated. Cluster analysis showed that these differentially expressed mRNA could effectively distinguish between the sham-operated group and the model group. Compared with the model group， the damage to testicular tissue in the Wuzi Yanzongwan group was reduced， the structure of the seminiferous tubules was intact， vacuolization was reduced， and the number of spermatogenic cells at all levels was significantly increased and arranged tightly. The serum T significantly increased， LH significantly decreased（P<0.01）， and FSH decreased but the difference was not statistically significant. The count and vitality of sperm in the epididymis were significantly increased（P<0.01）. Moreover， Wuzi Yanzongwan could regulate 159 mRNA levels in the testes of semi-castrated mice， of which 32 were up-regulated and 127 were down-regulated， and the data of the transcriptome assay was verified to be reliable by Real-time PCR. GO and KEGG analysis showed that the transcriptome functions regulated by Wuzi Yanzongwan were involved in the whole cell cycle process of sperm development such as sex hormone production of interstitial cells in testis， renewal， differentiation， metabolism， apoptosis and signal transduction of spermatogenic cells， and were closely related to the biological behaviors of signaling pathways such as spermatogenic stem cell function， endoplasmic reticulum protein processing and metabolic program. ConclusionWuzi Yanzongwan can effectively improve the low spermatogenic function of semi-castrated male mice， and its mechanism may be related to the regulation of testicular transcriptional regulatory network， the synthesis of sex hormones in testicular interstitial cells， the function of spermatogenic stem cells， the whole cell cycle process of spermatogenesis， as well as the expression of endoplasmic reticulum protein processing and metabolic program related genes transcription.

Objective To observe the effect of dapagliflozin on cardiac function in patients with heart failure after emergency percutaneous transluminal coronary intervention in acute ST segment elevation myocardial infarction. Methods A total of 100 patients with acute myocardial infarction underwent emergency PCI were randomly divided into study group (52 cases) and control group (48 cases). The study group was given dapagliflozin on the basis of standardized treatment of myocardial infarction, and the control group was given conventional treatment of myocardial infarction. Cardiac ultrasound related indexes[left ventricular ejection fraction (LVEF), left ventricular end-diastolic diameter (LVEDD), left ventricular end-systolic diameter (LVESD), left ventricular end-diastolic volume (LVEDV)], plasma N-terminal brain natriuretic peptide (NT-proBNP) level, 6-minute walking test (6MWT) results. The incidence of adverse reactions and major cardiovascular adverse events (MACE) were compared between the two groups during follow-up. Results After 6 months of treatment, LVESD, LVEDD and LVEDV in the two groups were significantly lower than before treatment, and LVEF was significantly higher than before treatment (P < 0.05); the LVESD, LVEDD and LVEDV of the study group were significantly lower than those of the control group, and LVEF was significantly higher than that of the control group (P < 0.05). The NT-proBNP in the two groups was significantly lower than before treatment, and was significantly lower in the study group than that in the control group (P < 0.05). The 6MWT distance of the study group was significantly longer than that of the control group (P < 0.05). There was no significant difference in the incidence of adverse reactions and MACE between the two groups (P>0.05). Conclusion Dapagliflozin can improve cardiac function in patients with heart failure after emergency PCI of acute ST segment elevation myocardial infarction.

Objective:To investigate the early and middle term clinical efficacies of 3D-printed metal prostheses in the reconstruction of bone defects after osteotomy in malignant bone tumors.Methods:A total of 34 patients with malignant bone tumors of lower extremity femur and tibia who underwent 3D printing individualized metal prosthesis replacement surgery in the Department of Bone and Soft Tissue of Affiliated Cancer Hospital of Zhengzhou University from March 2019 to March 2022 were retrospectively analyzed. There were 23 males and 11 females, with an average age of 19.1±15.2 years (range, 7-80 years). There were 22 children and adolescents younger than 18 years old. There were 3 cases in the proximal femur, 15 cases in the middle and distal femur, 10 cases in the proximal tibia and 6 cases in the distal tibia. According to the final pathological diagnosis, 24 cases of osteosarcoma, 6 cases of Ewing's sarcoma, 2 cases of undifferentiated sarcoma, 1 case of osteosarcoma, and 1 case of malignant giant cell tumor of bone were enrolled in this study. Postoperative complications, wound healing, periprosthetic fracture and aseptic loosening, tumor outcome (evaluated by tumor control evaluation criteria), and length difference of lower limbs were recorded. Response evaluation criteria in solid tumor (RECIST) was used to evaluate tumor outcomes. Prosthetic-bone interface healing was evaluated postoperatively, and the function was evaluated based on Musculoskeletal Oncology Society (MSTS) 93.Results:The length of lesions was 70-240 mm in 34 patients, with an average of 125.5±35.4 mm. The length of osteotomy was 80-275 mm, with an average of 160.2±33.9 mm. No tumor was found on the osteotomy surface. The customized prosthesis was firmly installed and closely matched with the side of the preserved articular surface. There were 2 patients with local incision fat liquefaction and 4 patients with superficial wound infection, which healed after debridement and antibiotic treatment. One distal tibia osteosarcoma case developed severe periprosthetic infection 2 months after surgery, resulting in prosthesis implantation failure, limb movement pain and poor ankle function. After removal of the prosthesis, infection control and osteogenesis with the Ilizarov technique, the infection was completely controlled and local osteogenesis was possible. The remaining 33 patients had a good prosthetic-bone interface union. One case was found to have localized bone resorption on the contact surface of the prosthesis 7 months after operation, but the metal prosthesis and screws were not loose. The incisions healed well in other patients, without infection, prosthesis loosening, fracture or other complications. All patients survived and were followed up for 13.8±5.6 months (range, 7-27 months). During the follow-up, there was no recurrence of tumor at the osteotomy end in all patients, but 5 patients developed lung metastasis. At the end of the last follow-up, all patients survived. Among them, 16 patients had unequal length of lower limbs, including 10 cases within 2 cm, 3 cases between 2-5 cm, and 3 cases over 5 cm. With the exception of one patient whose prosthesis was removed due to infection, the MSTS 93 of the other patients was 24.9±2.2 (range, 19-28), and were rated as excellent in 26 cases and good in 7 cases. According to the RECIST evaluation criteria, 26 of 34 patients had complete response, 5 had disease progression, and 3 had stable disease.Conclusion:3D printed metal prosthesis is one of the effective methods for the treatment of bone defects after resection of malignant bone tumors in lower limbs, which is safe, reliable and has satisfactory early curative effect.

Primary hyperoxaluria (PH) is a rare autosomal recessive hereditary disease, characterized by calcium oxalate kidney stone and nephrocalcinosis caused by defects in enzymes of liver glyoxylate metabolism. Up to now, treatment options for PH are limited. Although medication treatment and liver transplantation can slow down the progression and mitigate the symptoms, the evidence for them turned out to be weak. In recent years, breakthroughs in biotechnology provide novel promising directions for drug development. Small interfering RNA drugs, such as lumasiran and nedosiran, selectively reduce hepatic expression of glycolate oxidase and lactate dehydrogenase respectively, reducing hepatic oxalate production and urinary oxalate levels in PH patients. Gene-editing, such as CRISPR/Cas9, will be a potential treatment method of PH. This review encompasses recent developments in the gene therapy of PH.

Polyphyllin Ⅰ(PPⅠ)and polyphyllin Ⅱ(PⅡ)are the main active substances in the Paris polyphylla.However,liver toxicity of these compounds has impeded their clinical application and the potential hepatotoxicity mechanisms remain to be elucidated.In this work,we found that PPⅠ and PⅡ exposure could induce significant hepatotoxicity in human liver cell line L-02 and zebrafish in a dose-dependent manner.The results of the proteomic analysis in L-02 cells and transcriptome in zebrafish indicated that the hepa-totoxicity of PPⅡ and PⅡwas associated with the cholesterol biosynthetic pathway disorders,which were alleviated by the cholesterol biosynthesis inhibitor lovastatin.Additionally,3-hydroxy-3-methy-lglutaryl CoA reductase(HMGCR)and squalene epoxidase(SQLE),the two rate-limiting enzymes in the choles-terol synthesis,selected as the potential targets,were confirmed by the molecular docking,the over-expression,and knockdown of HMGCR or SQLE with siRNA.Finally,the pull-down and surface plasmon resonance technology revealed that PPⅠ could directly bind with SQLE but not with HMGCR.Collectively,these data demonstrated that PPⅠ-induced hepatotoxicity resulted from the direct binding with SQLE protein and impaired the sterol-regulatory element binding protein 2/HMGCR/SQLE/lanosterol synthase pathways,thus disturbing the cholesterol biosynthesis pathway.The findings of this research can contribute to a better understanding of the key role of SQLE as a potential target in drug-induced hepatotoxicity and provide a therapeutic strategy for the prevention of drug toxic effects with similar structures in the future.

Renal abscess caused by fish bone ingestion is extremely rare and has not been reported in the literature. A male patient presented with a 1-week history of flank pain and a 2-day history of fever. Urinary ultrasound and CT scan showed an irregular hypodense lesion in the left kidney and blurred thickening of the descending colon wall. Three-dimensional CT reconstruction images revealed a needle-like foreign body, which perforated from the descending colonic lumen to the left kidney. The patient had accidentally eaten fish bone one week prior. On the basis of clinical data, the diagnosis of renal abscess caused by foreign body was suspected. Accordingly, laparotomy was performed, the abscess was drained, and the colon was repaired. The foreign body was confirmed to be fish bone. The postoperative condition of the patient was uneventful, and the patient remained well in the 3 months' follow-up without any further complaints.

The prognosis for diffusely infiltrating gliomas at World Health Organization (WHO) grade 2-4 remains dismal due to their heterogeneity. The rapid development of genome-wide molecular-profiling-associated studies has greatly promoted the accuracy of glioma classification. Thus, the latest version of the WHO classification of the central nervous system tumors published in 2021 has incorporated more molecular biomarkers together with histological features for the diagnosis of gliomas. Advanced usage of molecular pathology in clinical diagnostic practice provides also new opportunities for the therapy of patients with glioma, including surgery, radiotherapy and chemotherapy, targeted therapy, immunotherapy, and more precision clinical trials. Herein, we highlight the updates in the classification of gliomas according to the latest WHO guidelines and summarize the clinically relevant molecular markers by focusing on their applications in clinical practice. We also review the advances in molecular features of gliomas, which can facilitate the development of glioma therapies, thereby discussing the challenges and future directions of molecular pathology toward precision medicine for patients with glioma.