1.EvoNB: A protein language model-based workflow for nanobody mutation prediction and optimization.
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):101260-101260
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.
2.Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults (version 2025)
Bobin MI ; Faqi CAO ; Weixian HU ; Wu ZHOU ; Chenchen YAN ; Hui LI ; Yun SUN ; Yuan XIONG ; Jinmi ZHAO ; Qikai HUA ; Xinbao WU ; Xieyuan JIANG ; Dianying ZHANG ; Zhongguo FU ; Dankai WU ; Guangyao LIU ; Guodong LIU ; Tengbo YU ; Jinhai TAN ; Xi CHEN ; Fengfei LIN ; Zhangyuan LIN ; Dongfa LIAO ; Aiguo WANG ; Shiwu DONG ; Gaoxing LUO ; Zhao XIE ; Dong SUN ; Dehao FU ; Yunfeng CHEN ; Changqing ZHANG ; Kun LIU ; Deye SONG ; Yongjun RUI ; Fei WU ; Ximing LIU ; Junwen WANG ; Meng ZHAO ; Biao CHE ; Bing HU ; Chengjian HE ; Guanglin WANG ; Xiao CHEN ; Guandong DAI ; Shiyuan FANG ; Wenchao SONG ; Ming CHEN ; Guanghua GUO ; Yongqing XU ; Lei YANG ; Wenqian ZHANG ; Kun ZHANG ; Xin TANG ; Hua CHEN ; Weiguo XU ; Shuquan GUO ; Yong LIU ; Xiaodong GUO ; Zhewei YE ; Liming XIONG ; Tian XIA ; Hongbin WU ; Qisheng ZHOU ; Mengfei LIU ; Yiqiang HU ; Yanjiu HAN ; Hang XUE ; Kangkang ZHA ; Wei CHEN ; Zhiyong HOU ; Bin YU ; Jiacan SU ; Peifu TANG ; Baoguo JIANG ; Guohui LIU
Chinese Journal of Trauma 2025;41(5):421-432
Postoperative infection of internal fixation of closed fractures the lower limbs in adults represents a devastating complication, characterized by diagnostic challenges, prolonged treatment duration and high disability rates. Current management of these infections faces multiple challenges, such as difficulties in early accurate diagnosis, and various controversies about the treatment plan, leading to poor overall diagnosis and treatment results. To address these issues, based on evidence-based medicine and principles with emphasis on scientific rigor, clinical applicability and innovation, the Trauma Branch of the Chinese Medical Association, Orthopedic Branch of the Chinese Medical Doctor Association, Orthopedics Branch of the Chinese Medical Association, and Trauma Orthopedics and Polytrauma Group of the Resuscitation and Emergency Committee of the Chinese Medical Doctor Association have collaboratively organized a panel of relevant experts to develop the Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults ( version 2025). The guideline proposed 10 recommendations, aiming to provide a foundation for standardized diagnosis and treatment of postoperative infection in adults with closed lower limb fractures.
3.EvoNB:A protein language model-based workflow for nanobody mutation prediction and optimization
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):1334-1343
The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic 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 work-flow,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 mu-tations to predict their impact on binding affinity to the targets.The results showed that multiple mu-tations 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.
4.Complete genomic sequence analysis of the G6P1bovine rotavirus BLL strain
Jin-hua ZHANG ; Xia-fei LIU ; Jun-jie YU ; Jia-xin FAN ; Ming-yue WANG ; Guang-ping XIONG ; Yi-peng WANG ; Dan-di LI ; Xiao-man SUN ; Li-li PANG ; Zhao-jun DUAN
Chinese Journal of Zoonoses 2025;41(1):8-14
Bovine rotavirus(BRV)is an important pathogen causing diarrhea in calves.To understand the genomic charac-teristics and genetic variations in bovine rotavirus,and to further enrich data on the biological characteristics of rotavirus,we aimed to amplify 11 gene segments of the isolated and cultured G6P[1]bovine rotavirus BLL strain,perform whole genome se-quencing,and analyze the molecular characteristics.MEGA7.0 and DNAMAN software were used for homology and typing a-nalysis,and the whole genome phylogenetic tree was constructed to analyze genetic evolution relationships.The complete geno-type of the BLL strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3.Phylogenetic analysis of the VP7 and VP4 genes of the BLL strain showed that the VP7 gene had the highest homology with RVA/Cow-wt/HB01/China/2021,and the VP4 gene of the BLL strain was in the same branch as RVA/Human-tc/ISR/Ro8059/1995.From the sequence alignment of VP8*amino acids,the sialic acid domain of the BLL strain was found to be similar to that in other P[1]strains,but different from those in other types of strains,except for residue 189,which was the same as that in Ro8059 but different from that in other strains.The results suggested that the BLL strain might potentially infect humans.Therefore,continued monitoring and study of the biological characteristics of this strain are necessary to provide more information and evidence supporting further research on the cross-species transmission of group A rotavirus in China.
5.Complete genomic sequence analysis of the G6P1bovine rotavirus BLL strain
Jin-hua ZHANG ; Xia-fei LIU ; Jun-jie YU ; Jia-xin FAN ; Ming-yue WANG ; Guang-ping XIONG ; Yi-peng WANG ; Dan-di LI ; Xiao-man SUN ; Li-li PANG ; Zhao-jun DUAN
Chinese Journal of Zoonoses 2025;41(1):8-14
Bovine rotavirus(BRV)is an important pathogen causing diarrhea in calves.To understand the genomic charac-teristics and genetic variations in bovine rotavirus,and to further enrich data on the biological characteristics of rotavirus,we aimed to amplify 11 gene segments of the isolated and cultured G6P[1]bovine rotavirus BLL strain,perform whole genome se-quencing,and analyze the molecular characteristics.MEGA7.0 and DNAMAN software were used for homology and typing a-nalysis,and the whole genome phylogenetic tree was constructed to analyze genetic evolution relationships.The complete geno-type of the BLL strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3.Phylogenetic analysis of the VP7 and VP4 genes of the BLL strain showed that the VP7 gene had the highest homology with RVA/Cow-wt/HB01/China/2021,and the VP4 gene of the BLL strain was in the same branch as RVA/Human-tc/ISR/Ro8059/1995.From the sequence alignment of VP8*amino acids,the sialic acid domain of the BLL strain was found to be similar to that in other P[1]strains,but different from those in other types of strains,except for residue 189,which was the same as that in Ro8059 but different from that in other strains.The results suggested that the BLL strain might potentially infect humans.Therefore,continued monitoring and study of the biological characteristics of this strain are necessary to provide more information and evidence supporting further research on the cross-species transmission of group A rotavirus in China.
6.Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults (version 2025)
Bobin MI ; Faqi CAO ; Weixian HU ; Wu ZHOU ; Chenchen YAN ; Hui LI ; Yun SUN ; Yuan XIONG ; Jinmi ZHAO ; Qikai HUA ; Xinbao WU ; Xieyuan JIANG ; Dianying ZHANG ; Zhongguo FU ; Dankai WU ; Guangyao LIU ; Guodong LIU ; Tengbo YU ; Jinhai TAN ; Xi CHEN ; Fengfei LIN ; Zhangyuan LIN ; Dongfa LIAO ; Aiguo WANG ; Shiwu DONG ; Gaoxing LUO ; Zhao XIE ; Dong SUN ; Dehao FU ; Yunfeng CHEN ; Changqing ZHANG ; Kun LIU ; Deye SONG ; Yongjun RUI ; Fei WU ; Ximing LIU ; Junwen WANG ; Meng ZHAO ; Biao CHE ; Bing HU ; Chengjian HE ; Guanglin WANG ; Xiao CHEN ; Guandong DAI ; Shiyuan FANG ; Wenchao SONG ; Ming CHEN ; Guanghua GUO ; Yongqing XU ; Lei YANG ; Wenqian ZHANG ; Kun ZHANG ; Xin TANG ; Hua CHEN ; Weiguo XU ; Shuquan GUO ; Yong LIU ; Xiaodong GUO ; Zhewei YE ; Liming XIONG ; Tian XIA ; Hongbin WU ; Qisheng ZHOU ; Mengfei LIU ; Yiqiang HU ; Yanjiu HAN ; Hang XUE ; Kangkang ZHA ; Wei CHEN ; Zhiyong HOU ; Bin YU ; Jiacan SU ; Peifu TANG ; Baoguo JIANG ; Guohui LIU
Chinese Journal of Trauma 2025;41(5):421-432
Postoperative infection of internal fixation of closed fractures the lower limbs in adults represents a devastating complication, characterized by diagnostic challenges, prolonged treatment duration and high disability rates. Current management of these infections faces multiple challenges, such as difficulties in early accurate diagnosis, and various controversies about the treatment plan, leading to poor overall diagnosis and treatment results. To address these issues, based on evidence-based medicine and principles with emphasis on scientific rigor, clinical applicability and innovation, the Trauma Branch of the Chinese Medical Association, Orthopedic Branch of the Chinese Medical Doctor Association, Orthopedics Branch of the Chinese Medical Association, and Trauma Orthopedics and Polytrauma Group of the Resuscitation and Emergency Committee of the Chinese Medical Doctor Association have collaboratively organized a panel of relevant experts to develop the Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults ( version 2025). The guideline proposed 10 recommendations, aiming to provide a foundation for standardized diagnosis and treatment of postoperative infection in adults with closed lower limb fractures.
7.Advances of ceftazidime/avibactam in the treatment of carbapenem-resis-tant Klebsiella pneumoniae infection
Yuan-Qi ZHAO ; Ming-Jing CHENG ; Miao-Miao XIONG ; Min XIAO ; Xiu-Yu CUI ; Zi-Jian ZHOU ; Yi-Wei YU ; Wei-Dong ZHAO
Chinese Journal of Infection Control 2024;23(8):1047-1052
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.
8.Risk Factors of Late-Onset Hemorrhagic Cystitis after Allogeneic Hematopoietic Stem Cell Transplantation
Lin-Yi ZHANG ; Yi-Ying XIONG ; Ming-Yan LIAO ; Qing XIAO ; Xiao-Qiong TANG ; Xiao-Hua LUO ; Hong-Bin ZHANG ; Li WANG ; Lin LIU
Journal of Experimental Hematology 2024;32(1):250-256
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.
9.Risk Factors of Primary Poor Graft Function after Allogeneic Hematopoietic Stem Cell Transplantation in Patients with Myeloid Malignancies
Lin-Yi ZHANG ; Yi-Ying XIONG ; Ming-Yan LIAO ; Qing XIAO ; Xiao-Qiong TANG ; Xiao-Hua LUO ; Hong-Bin ZHANG ; Li WANG ; Lin LIU
Journal of Experimental Hematology 2024;32(6):1875-1881
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.
10.Effect of'Wenyang Tongmai'Moxibustion on the Inflammatory Response of ApoE-/-Atherosclerotic Mice Based on the SIRT1/FOXO3a Signaling Pathway
Jiao-Jiao XIONG ; Xian-Ming WU ; Chao-Bo YAN ; Ning ZHANG ; Zhou ZHU ; Li PAN ; Xiao-Fang YANG
Journal of Guangzhou University of Traditional Chinese Medicine 2024;41(9):2410-2417
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.

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