The identification and optimization of mutations in nanobodies are crucial for enhancing their therapeutic potential in disease prevention and control. However, this process is often complex and time-consuming, which limit its widespread application in practice. In this study, we developed a workflow, named Evolutionary-Nanobody (EvoNB), to predict key mutation sites of nanobodies by combining protein language models (PLMs) and molecular dynamic (MD) simulations. By fine-tuning the ESM2 model on a large-scale nanobody dataset, the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced. The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies. Additionally, we selected four widely representative nanobody-antigen complexes to verify the predicted effects of mutations. MD simulations analyzed the energy changes caused by these mutations to predict their impact on binding affinity to the targets. The results showed that multiple mutations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target, further validating the potential of this workflow for designing and optimizing nanobody mutations. Additionally, sequence-based predictions are generally less dependent on structural absence, allowing them to be more easily integrated with tools for structural predictions, such as AlphaFold 3. Through mutation prediction and systematic analysis of key sites, we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes. The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.

Objective To establish a renal cell co-culture system to simulate the renal barrier system,and to test its responsiveness to different glucose concentrations,and to investigate the regulatory effect of miR-29b-3p on osteopontin(OPN)/transforming growth factor β(TGF-β)pathway and the changes of this pathway under high glucose condition.Methods The three-cell co-culture system consisting of human renal podocytes,human glomerular mesangial cells and human renal tubular epithelial cells was established to test the cell viability and glucose consumption value at glucose concentrations of 5,8,12 and 16 mmol/L.The content of TGF-β and OPN in cell supernatant was measured.The recombinant plasmid and siRNA of OPN were transfected,and the expressions of TGF-β and OPN were detected by Q-PCR and Western blot.Results The mRNA expressions of OPN,TGF-β and miR-29b were significantly increased at 12 mmol/L glucose conditions.Western blot results showed that the protein expression of OPN increased in high glucose conditions,while the protein expression of TGF-β did not change significantly.After adding miR-29b-3p activator,the mRNA levels of OPN and TGF-β in the cell supernatant were significantly increased.After adding miR-29b-3p inhibitor,the mRNA levels of OPN and TGF-β in the cell supernatant were significantly decreased.Western blot results showed that compared with 5 mmol/L glucose,the protein expressions of OPN and TGF-β were increased by miR-29b-3p activator,and the protein expressions of OPN and TGF-β were decreased by miR-29b-3p inhibitor.After transfection with OPN recombinant plasmid,the content of TGF-β in the cell supernatant was significantly increased,and the mRNA expressions of OPN and TGF-β in the cells were significantly increased.After transfection with OPN siRNA,the content of TGF-β in the cell supernatant was decreased,and the expression of OPN mRNA in the cells was significantly decreased,but the expression of TGF-β mRNA was not significantly increased.Conclusion The renal cell co-culture system can mimic the complex renal environment in vivo.When induced by high glucose,cell proliferation is inhibited,glucose consumption is increased,and the content of TGF-β in the cell supernatant is increased,and miR-29b-3p has a regulatory effect on OPN/TGF-β signaling pathway in the co-culture system.

Objective:To analyze the risk factors for late-onset hemorrhagic cystitis(LOHC)after allogeneic hematopoietic stem cell transplantation(allo-HSCT),the risk factors for the progression of LOHC to severe LOHC,and the effect of LOHC on survival.Methods:The clinical data of 300 patients who underwent allo-HSCT at the First Affiliated Hospital of Chongqing Medical University from January 2015 to December 2021 were retrospectively analyzed.The relevant clinical parameters that may affect the occurance of LOHC after allo-HSCT were selected for univariate and multivariate analysis.Then,the differences in overall survival(OS)and progression-free survival(PFS)between different groups were analyzed.Results:The results of multivariate analysis showed that the independent risk factors for LOHC after allo-HSCT were as follows:age≤45 years old(P=0.039),intensified conditioning regimen with fludarabine/cladribine and cytarabine(P=0.002),albumin ≤ 30 g/L on d30 after transplantation(P=0.007),CMV-DNA positive(P=0.028),fungal infection before transplantation(P=0.026),and the occurrence of grade Ⅱ-Ⅳ aGVHD(P=0.006).In the transplant patients who have already developed LOHC,the occurance of LOHC within 32 days after transplantation(P=0.008)and albumin ≤ 30 g/L on d30 after transplantation(P=0.032)were independent risk factors for the progression to severe LOHC.The OS rate of patients with severe LOHC was significantly lower than that of patients without LOHC(P=0.041).Conclusion:For the patients aged ≤ 45 years old and with intensified conditioning regimen,it is necessary to be vigilant about the occurrence of LOHC;For the patients with earlier occurrence of LOHC,it is necessary to be vigilant that it develops into severe LOHC.Early prevention and treatment of LOHC are essential.Regular monitoring of CMV-DNA and albumin levels,highly effective antiviral and antifungal therapies,and prevention of aGVHD are effective measures to prevent the occurrence and development of LOHC.

Objective:To analyze the risk factors of primary poor graft function (PGF) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in patients with myeloid malignancies and the impact of primary PGF on survival. Methods:The clinical data of 146 patients with myeloid malignancies who underwent allo-HSCT in our hospital from January 2015 to December 2021 were retrospectively studied. Some relevant clinical parameters which may affect the development of primary PGF after allo-HSCT were selected for univariate and multivariate analysis,as well as performed survival analysis. Results:A total of 9 patients (6.16％) were diagnosed with primary PGF,and their medium age was 37(28-53) years old. Among them,1 case underwent matched sibling donor HSCT,1 case underwent matched unrelated donor HSCT,and 7 cases underwent HLA-haploidentical related donor HSCT. Moreover,5 cases were diagnosed as cytomegalovirus (CMV) infection,and 3 cases as Epstein-Barr virus (EBV) infection. Univariate and multivariate analysis showed that CD34+cell dose<5×106/kg and pre-transplant C-reactive protein (CRP)>10 mg/L were independent risk factors for occurrence of the primary PGF after allo-HSCT in patients with myeloid malignancies. The 3-year overall survival (OS) rate of primary PGF group was 52.5％,which was significantly lower than 82.8％ of good graft function group (P<0.05). Conclusion:Making sure pre-transplant CRP≤10 mg/L and CD34+cell dose ≥5×106/kg in the graft may have an effect on preventing the occurrence of primary PGF after allo-HSCT. The occurrence of primary PGF may affect the OS rate of transplant patients,and early prevention and treatment are required.

Objective To explore the mechanism of'Wenyang Tongmai'(warming yang to unblock meridians)moxibustion in preventing and treating atherosclerosis.Methods Ten C57BL/6J mice fed with normal diet were set as blank group.Thirty ApoE-/-mice were fed with high-fat diet to establish atherosclerosis model,and were randomly divided into model group,Simvastatin group and moxibustion group,with 10 mice in each group.The intervention began on the first day of modeling.The mice in the moxibustion group were given moxibustion at Danzhong(RN17),Shenque(RN8),Neiguan(PC6),Xuehai(SP10)points,and the Simvastatin group was given Simvastatin distilled water suspension by gavage for 12 weeks.After administration,the pathological structure of thoracic aorta in mice was observed by hematoxylin-eosin(HE)staining method.The ultrastructure of thoracic aortic endothelial cells in mice was observed by transmission electron microscopy.The levels of serum tumor necrosis factor α(TNF-α),intercellular adhesion molecule 1(ICAM-1)and vascular cell adhesion molecule 1(VCAM-1)in mice were detected by enzyme-linked immunosorbent assay(ELISA).The mRNA expression levels of silent information regulator 1(SIRT1)and forkhead box O3a(FOXO3a)in thoracic aorta were detected by real-time quantitative polymerase chain reaction(qRT-PCR).The protein expression levels of SIRT1 and FOXO3a in thoracic aorta were detected by Western Blot.Results Compared with the blank group,the pathological changes of thoracic aorta and vascular endothelial cells in the model group were obvious,the levels of serum inflammatory factor TNF-α,ICAM-1 and VCAM-1 were increased(P＜0.05 or P＜0.01),the mRNA and protein expressions of SIRT1 in thoracic aorta were decreased(P＜0.01),and the mRNA and protein expressions of FOXO3a had no significant difference(P＞0.05).Compared with the model group,the thoracic aorta and vascular endothelial cell structure of the mice in the Simvastatin group and the moxibustion group were obviously improved,the levels of serum TNF-α,ICAM-1 and VCAM-1 were decreased(P＜0.05),the mRNA and protein expressions of SIRT1 in the thoracic aorta were increased(P＜0.05 or P＜0.01),and the mRNA and protein expressions of FOXO3a had no significant difference(P＞0.05).There was no significant difference in the above indexes between the Simvastatin group and the moxibustion group(P＞0.05).Conclusion'Wenyang Tongmai'moxibustion can prevent and treat atherosclerotic in rats via regulating and controlling SIRT1/FOXO3a signaling pathway to reduce inflammatory response.

In recent years,the prevalence of carbapenem-resistant Klebsiella pneumoniae(CRKP)infection has become a global public health issue.Ceftazidime/avibactam(CAZ/AVI)has been approved as a novel antimicrobial agent for the treatment of healthcare-associated pneumonia/ventilator-associated pneumonia,bloodstream infection,infection after kidney transplantation,and severe infection combined with liver cirrhosis.However,the use of CAZ/AVI has also led to the emergence of drug-resistant strains.The major mechanisms of drug-resistance include over-expression of blaKPC gene,mutation of β-lactamase and amino acids at key sites,changes in cell permeability caused by loss of membrane porin,and over-expression of efflux pump.This article reviews the research progress of CAZ/AVI in the treatment of CRKP infection,providing reference for clinical diagnosis and treatment.

Objective A recombinant plasmid for CRISPR interference(CRISPRi)that incorporates dCas9 from Streptococcus pyogenes was constructed to investigate the function of Coxiella burnetii genes through a prompt,simple method.Methods A single guide RNA(sgRNA)sequence targeting C.burnetii dotB was integrated into a recombinant plasmid,which was then transformed into C.burnetii using electroporation.Next,dCas9 expression was induced with dehydrated tetracycline(aTC)to inhibit the transcription of dotB.Results The results demonstrated that dCas9 can be expressed normally in the CRISPRi system through aTC induction.Suppression of dotB was observed at the transcriptional and translational levels.In addition,the intracellular reproduction of C.burnetii significantly decreased after the suppression of dotB expression.Conclusion Silencing technology for the C.burnetii gene based on CRISPRi was established in this study,providing support for studying the biological functions of C.burnetii genes.

This study explored the protective effect of astragaloside Ⅳ(AS-Ⅳ) on oxygen-glucose deprivation(OGD)-induced autophagic injury in PC12 cells and its underlying mechanism. An OGD-induced autophagic injury model in vitro was established in PC12 cells. The cells were divided into a normal group, an OGD group, low-, medium-, and high-dose AS-Ⅳ groups, and a positive drug dexmedetomidine(DEX) group. Cell viability was measured using the MTT assay. Transmission electron microscopy was used to observe autophagosomes and autolysosomes, and the MDC staining method was used to assess the fluorescence intensity of autophagosomes. Western blot was conducted to determine the relative expression levels of functional proteins LC3-Ⅱ/LC3-Ⅰ, Beclin1, p-Akt/Akt, p-mTOR/mTOR, and HIF-1α. Compared with the normal group, the OGD group exhibited a significant decrease in cell viability(P<0.01), an increase in autophagosomes(P<0.01), enhanced fluorescence intensity of autophagosomes(P<0.01), up-regulated Beclin1, LC3-Ⅱ/LC3-Ⅰ, and HIF-1α(P<0.05 or P<0.01), and down-regulated p-Akt/Akt and p-mTOR/mTOR(P<0.05 or P<0.01). Compared with the OGD group, the low-and medium-dose AS-Ⅳ groups and the DEX group showed a significant increase in cell viability(P<0.01), decreased autophagosomes(P<0.01), weakened fluorescence intensity of autophagosomes(P<0.01), down-regulated Beclin1, LC3-Ⅱ/LC3-Ⅰ, and HIF-1α(P<0.05 or P<0.01), and up-regulated p-Akt/Akt and p-mTOR/mTOR(P<0.01). AS-Ⅳ at low and medium doses exerted a protective effect against OGD-induced autophagic injury in PC12 cells by activating the Akt/mTOR pathway, subsequently influencing HIF-1α. The high-dose AS-Ⅳ group did not show a statistically significant difference compared with the OGD group. This study provides a certain target reference for the prevention and treatment of OGD-induced cellular autophagic injury by AS-Ⅳ and accumulates laboratory data for the secondary development of Astragali Radix and AS-Ⅳ.
Rats ; Animals ; PC12 Cells ; Proto-Oncogene Proteins c-akt/genetics* ; Glucose/therapeutic use* ; Oxygen/metabolism* ; Beclin-1/pharmacology* ; TOR Serine-Threonine Kinases/metabolism* ; Autophagy ; Apoptosis ; Reperfusion Injury/drug therapy*

Humans ; Female ; Breast Neoplasms

Humans ; Otitis Media, Suppurative ; Chronic Disease ; Biofilms ; Otitis Media