In this study,the structural characters,antioxidant activities and bile acid-binding ability of sea buckthorn polysaccharides(HRPs)obtained by the commonly used hot water(HRP-W),pressurized hot water(HRP-H),ultrasonic...In this study,the structural characters,antioxidant activities and bile acid-binding ability of sea buckthorn polysaccharides(HRPs)obtained by the commonly used hot water(HRP-W),pressurized hot water(HRP-H),ultrasonic(HRP-U),acid(HRP-C)and alkali(HRP-A)assisted extraction methods were investigated.The results demonstrated that extraction methods had significant effects on extraction yield,monosaccharide composition,molecular weight,particle size,triple-helical structure,and surface morphology of HRPs except for the major linkage bands.Thermogravimetric analysis showed that HRP-U with filamentous reticular microstructure exhibited better thermal stability.The HRP-A with the lowest molecular weight and highest arabinose content possessed the best antioxidant activities.Moreover,the rheological analysis indicated that HRPs with higher galacturonic acid content and molecular weight showed higher viscosity and stronger crosslinking network(HRP-C,HRP-W and HRP-U),which exhibited stronger bile acid binding capacity.The present findings provide scientific evidence in the preparation technology of sea buckthorn polysaccharides with good antioxidant and bile acid binding capacity which are related to the structure affected by the extraction methods.展开更多
Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as bioch...Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.展开更多
Reliable calculations of nuclear binding energies are crucial for advancing the research of nuclear physics. Machine learning provides an innovative approach to exploring complex physical problems. In this study, the ...Reliable calculations of nuclear binding energies are crucial for advancing the research of nuclear physics. Machine learning provides an innovative approach to exploring complex physical problems. In this study, the nuclear binding energies are modeled directly using a machine-learning method called the Gaussian process. First, the binding energies for 2238 nuclei with Z > 20 and N > 20 are calculated using the Gaussian process in a physically motivated feature space, yielding an average deviation of 0.046 MeV and a standard deviation of 0.066 MeV. The results show the good learning ability of the Gaussian process in the studies of binding energies. Then, the predictive power of the Gaussian process is studied by calculating the binding energies for 108 nuclei newly included in AME2020. The theoretical results are in good agreement with the experimental data, reflecting the good predictive power of the Gaussian process. Moreover, the α-decay energies for 1169 nuclei with 50 ≤ Z ≤ 110 are derived from the theoretical binding energies calculated using the Gaussian process. The average deviation and the standard deviation are, respectively, 0.047 MeV and 0.070 MeV. Noticeably, the calculated α-decay energies for the two new isotopes ^ (204 )Ac(Huang et al. Phys Lett B 834, 137484(2022)) and ^ (207) Th(Yang et al. Phys Rev C 105, L051302(2022)) agree well with the latest experimental data. These results demonstrate that the Gaussian process is reliable for the calculations of nuclear binding energies. Finally, the α-decay properties of some unknown actinide nuclei are predicted using the Gaussian process. The predicted results can be useful guides for future research on binding energies and α-decay properties.展开更多
Pentatricopeptide repeat(PPR)proteins represent one of the largest protein families in plants and typically localize to organelles like mitochondria and chloroplasts.By contrast,CYTOPLASMLOCALIZED PPR1(OsCPPR1)is a cy...Pentatricopeptide repeat(PPR)proteins represent one of the largest protein families in plants and typically localize to organelles like mitochondria and chloroplasts.By contrast,CYTOPLASMLOCALIZED PPR1(OsCPPR1)is a cytoplasm-localized PPR protein that can degrade OsGOLDENLIKE1(OsGLK1)mRNA in the tapetum of rice anther.However,the mechanism,by which OsCPPR1 recognizes and binds to OsGLK1 transcripts,remains unknown.Through protein structure prediction and macromolecular docking experiments,we observed that distinct PPR motif structures of OsCPPR1 exhibited varying binding efficiencies to OsGLK1 RNA.Moreover,RNA-electrophoretic mobility shift assay experiment demonstrated that the recombinant OsCPPR1 can directly recognize and bind to OsGLK1 mRNA in vitro.This further confirmed that the mutations in the conserved amino acids in each PPR motif resulted in loss of activity,while truncation of OsCPPR1 decreased its binding efficiency.These findings collectively suggest that it may require some co-factors to assist in cleavage,a facet that warrants further exploration in subsequent studies.展开更多
Gut microbiota plays an important role in food allergy.The immunoglobulin G(IgG)/immunoglobulin E(IgE)binding capacity and human gut microbiota changes of digestion products derived from glycated ovalbumin(OVA)were in...Gut microbiota plays an important role in food allergy.The immunoglobulin G(IgG)/immunoglobulin E(IgE)binding capacity and human gut microbiota changes of digestion products derived from glycated ovalbumin(OVA)were investigated.Gastrointestinal digestion effectively destroyed the primary structure of glycated OVA,resulting in a significantly higher digestibility than gastric digestion,and more abundant peptides<3 kDa.Moreover,gastric and gastrointestinal digestion products have different fluorescence quenching and red shift of fluorescence peaks,and possess different conformational structures.These changes resulted in a decrease in 28.7%of the IgE binding capacity of gastrointestinal digestion products beyond that of pepsin.Moreover,gastrointestinal digestion products of glycated OVA increased significantly the proportion of Subdoligranulum,Collinsella,and Bifidobacterium.Therefore,gastrointestinal digestion products of glycated OVA altered human intestinal microbiota,reducing the risk of potential allergy.展开更多
Colorectal cancer(CRC)ranks third in the number of cancers mainly because of the inability to diagnose it at an early stage.The pathogenesis of CRC is complicated,which is the result of the complex interaction of mult...Colorectal cancer(CRC)ranks third in the number of cancers mainly because of the inability to diagnose it at an early stage.The pathogenesis of CRC is complicated,which is the result of the complex interaction of multiple genetic and environmental factors.Currently,one of the main treatments for CRC is chemotherapy.But the primary cause of CRC treatment failure is drug resistance.The expression of cyclin-dependent kinase 9(CDK9)was correlated with elevated autophagy levels in colon cancer,and high expression of CDK9 indicates a poor prognosis in CRC.The incidence of autophagy and the expressions of Beclin 1 and ATP binding cassette transporter G2 are different in left and right colon cancer,and autophagy may be involved in the occurrence of chemotherapy resistance.In this article,the roles of CDK9,ATP binding cassette transporter G2 and Beclin 1 in CRC were elucidated,emphasizing the linkages among them and providing potential therapeutic targets of CRC.展开更多
BACKGROUND The intricate relationship between type 2 diabetes mellitus(T2DM)and diabetic nephropathy(DN)presents a challenge in understanding the significance of various biomarkers in diagnosis.AIM To elucidate the ro...BACKGROUND The intricate relationship between type 2 diabetes mellitus(T2DM)and diabetic nephropathy(DN)presents a challenge in understanding the significance of various biomarkers in diagnosis.AIM To elucidate the roles and diagnostic values ofα2-macroglobulin(α2-MG),podocalyxin(PCX),α-L-fucosidase(AFU),retinol-binding protein-4(RBP-4),and cystatin C(CysC)in DN.METHODS From December 2018 to December 2020,203 T2DM patients were enrolled in the study.Of these,115 were diagnosed with DN(115 patients),while the remaining 88 patients were classified as non-DN.The urinary levels ofα2-MG,PCX,and AFU and the serum concentrations RBP-4 and CysC were measured in conjunction with other relevant clinical indicators to evaluate their potential correlations and diagnostic utility.RESULTS After adjustments for age and gender,significant positive correlations were observed between the biomarkers CysC,RBP-4,α2-MG/urinary creatinine(UCr),PCX/UCr,and AFU/UCr,and clinical indicators such as urinary albumin-to-creatinine ratio(UACR),serum creatinine,urea,24-h total urine protein,and neutrophil-to-lymphocyte ratio(NLR).Conversely,these biomarkers exhibited negative correlations with the estimated glomerular filtration rate(P<0.05).Receiver operating characteristic(ROC)curve analysis further demonstrated the diagnostic performance of these biomarkers,with UACR showcasing the highest area under the ROC curve(AUC^(ROC))at 0.97.CONCLUSION This study underscores the diagnostic significance ofα2-MG,PCX,and AFU in the development of DN.The biomarkers RBP-4,CysC,PCX,AFU,andα2-MG provide promising diagnostic insights,while UACR is the most potent diagnostic biomarker in assessing DN.展开更多
BACKGROUND Hepatocellular carcinoma(HCC)is an aggressive subtype of liver cancer and is one of the most common cancers with high mortality worldwide.Reprogrammed lipid metabolism plays crucial roles in HCC cancer cell...BACKGROUND Hepatocellular carcinoma(HCC)is an aggressive subtype of liver cancer and is one of the most common cancers with high mortality worldwide.Reprogrammed lipid metabolism plays crucial roles in HCC cancer cell survival,growth,and evolution.Emerging evidence suggests the importance of fatty acid binding proteins(FABPs)in contribution to cancer progression and metastasis;however,how these FABPs are dysregulated in cancer cells,especially in HCC,and the roles of FABPs in cancer progression have not been well defined.AIM To understand the genetic alterations and expression of FABPs and their associated cancer hallmarks and oncogenes in contributing to cancer malignancies.METHODS We used The Cancer Genome Atlas datasets of pan cancer and liver hepatocellular carcinoma(LIHC)as well as patient cohorts with other cancer types in this study.We investigated genetic alterations of FABPs in various cancer types.mRNA expression was used to determine if FABPs are abnormally expressed in tumor tissues compared to non-tumor controls and to investigate whether their expression correlates with patient clinical outcome,enriched cancer hallmarks and oncogenes previously reported for patients with HCC.We determined the protein levels of FABP5 and its correlated genes in two HCC cell lines and assessed the potential of FABP5 inhibition in treating HCC cells.RESULTS We discovered that a gene cluster including five FABP family members(FABP4,FABP5,FABP8,FABP9 and FABP12)is frequently co-amplified in cancer.Amplification,in fact,is the most common genetic alteration for FABPs,leading to overexpression of FABPs.FABP5 showed the greatest differential mRNA expression comparing tumor with non-tumor tissues.High FABP5 expression correlates well with worse patient outcomes(P<0.05).FABP5 expression highly correlates with enrichment of G2M checkpoint(r=0.33,P=1.1e-10),TP53 signaling pathway(r=0.22,P=1.7e-5)and many genes in the gene sets such as CDK1(r=0.56,P=0),CDK4(r=0.49,P=0),and TP53(r=0.22,P=1.6e-5).Furthermore,FABP5 also correlates well with two co-expressed oncogenes PLK1 and BIRC5 in pan cancer especially in LIHC patients(r=0.58,P=0;r=0.58,P=0;respectively).FABP5high Huh7 cells also expressed higher protein levels of p53,BIRC5,CDK1,CDK2,and CDK4 than FABP5low HepG2 cells.FABP5 inhibition more potently inhibited the tumor cell growth in Huh7 cells than in HepG2 cells.CONCLUSION We discovered that FABP5 gene is frequently amplified in cancer,especially in HCC,leading to its significant elevated expression in HCC.Its high expression correlates well with worse patient outcome,enriched cancer hallmarks and oncogenes in HCC.FABP5 inhibition impaired the cell viability of FABP5high Huh7 cells.All these support that FABP5 is a novel therapeutic target for treating FABP5high HCC.展开更多
BACKGROUND Thrombocytopenia 2,an autosomal dominant inherited disease characterized by moderate thrombocytopenia,predisposition to myeloid malignancies and normal platelet size and function,can be caused by 5’-untran...BACKGROUND Thrombocytopenia 2,an autosomal dominant inherited disease characterized by moderate thrombocytopenia,predisposition to myeloid malignancies and normal platelet size and function,can be caused by 5’-untranslated region(UTR)point mutations in ankyrin repeat domain containing 26(ANKRD26).Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1)have been identified as negative regulators of ANKRD26.However,the positive regulators of ANKRD26 are still unknown.AIM To prove the positive regulatory effect of GATA binding protein 2(GATA2)on ANKRD26 transcription.METHODS Human induced pluripotent stem cells derived from bone marrow(hiPSC-BM)INTRODUCTION Ankyrin repeat domain containing protein 26(ANKRD26)acts as a regulator of adipogenesis and is involved in the regulation of feeding behavior[1-3].The ANKRD26 gene is located on chromosome 10 and shares regions of homology with the primate-specific gene family POTE.According to the Human Protein Atlas database,the ANKRD26 protein is localized to the Golgi apparatus and vesicles,and its expression can be detected in nearly all human tissues[4].Moreover,UniProt annotation revealed that ANKRD26 is localized in the centrosome and contains coiled-coil domains formed by spectrin helices and ankyrin repeats[5,6].The most common disease related to ANKRD26 is thrombocytopenia 2(THC2),which is a rare autosomal dominant inherited disease characterized by lifelong mild-to-moderate thrombocytopenia and mild bleeding[7-9].Caused by the variants in the 5’-untranslated region(UTR)of ANKRD26,THC2 is defined by a decrease in the number of platelets in circulating blood and results in increased bleeding and decreased clotting ability[8,10].Due to the point mutations that occur in the 5’-UTR of ANKRD26,its negative transcription factors(TFs),Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1),lose their repression effect[11].The persistent expression of ANKRD26 increases the activity of the mitogen activated protein kinase and extracellular signal regulated kinase 1/2 signaling pathways,which are potentially involved in the regulation of thrombopoietin-dependent signaling and further impair proplatelet formation by megakaryocytes(MKs)[11].However,the positive regulators of ANKRD26,which might be associated with THC2 pathology,are still unknown.展开更多
Hydrophobic Val derivative Schiff base copper(II) complexes and dipeptide (AlaAla, GlyGly) derivative Schiff base copper(II) complexes were introduced into egg white lysozyme. X-ray crystal structure analysis revealed...Hydrophobic Val derivative Schiff base copper(II) complexes and dipeptide (AlaAla, GlyGly) derivative Schiff base copper(II) complexes were introduced into egg white lysozyme. X-ray crystal structure analysis revealed amino acid derivative Schiff base copper(II) complexes were obtained. Herein we discuss primarily on the binding mode of copper(II) of the complexes obtained with egg white lysozyme. The electron density of copper(II) ions was confirmed by X-ray crystal structure analysis. The Val derivative Schiff base copper(II) complex was weakly bound at Arg114 of egg white lysozyme. In other copper(II) complexes, binding of copper(II) ions with dissociated ligands to various residues was observed. The binding sites of copper(II) ions were compared with computational scientific predictions.展开更多
BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetica...BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetically targeting some genes.Our study will examine the expression,potential effect,biological function and clinical value of SYNCRIP in CRC.AIM To examine the expression,potential effect,biological function and clinical value METHODS The expression of SYNCRIP was examined by immunohistochemistry arrays and high-throughput data.The effect of SYNCRIP gene in CRC cell growth was evaluated by CRISPR-Cas9 technology.The target genes of SYNCRIP were calculated using various algorithms,and the molecular mechanism of SYNCRIP in CRC was explored by mutation analysis and pathway analysis.The clinical value of SYNCRIP in prognosis and radiotherapy was revealed via evidence-based medicine methods.RESULTS The protein and mRNA levels of SYNCRIP were both highly expressed in CRC samples compared to nontumorous tissue based on 330 immunohistochemistry arrays and 3640 CRC samples.Cells grew more slowly in eleven CRC cell lines after knocking out the SYNCRIP gene.SYNCRIP could epigenetically target genes to promote the occurrence and development of CRC by boosting the cell cycle and affecting the tumor microenvironment.In addition,CRC patients with high SYNCRIP expression are more sensitive to radiotherapy.CONCLUSION SYNCRIP is upregulated in CRC,and highly expressed SYNCRIP can accelerate CRC cell division by exerting its epigenetic regulatory effects.In addition,SYNCRIP is expected to become a potential biomarker to predict the effect of radiotherapy.展开更多
In this paper, we consider the relationship between the binding number and the existence of fractional k-factors of graphs. The binding number of G is defined by Woodall as bind(G)=min{ | NG(X) || X |:∅≠X⊆V(G) }. It ...In this paper, we consider the relationship between the binding number and the existence of fractional k-factors of graphs. The binding number of G is defined by Woodall as bind(G)=min{ | NG(X) || X |:∅≠X⊆V(G) }. It is proved that a graph G has a fractional 1-factor if bind(G)≥1and has a fractional k-factor if bind(G)≥k−1k. Furthermore, it is showed that both results are best possible in some sense.展开更多
The basis functions of the translation invariant shell model are used to construct the ground state nuclear wave functions of <sup>3</sup>H. The used residual two-body interactions consist of central, tens...The basis functions of the translation invariant shell model are used to construct the ground state nuclear wave functions of <sup>3</sup>H. The used residual two-body interactions consist of central, tensor, spin orbit and quadratic spin orbit terms with Gaussian radial dependence. The parameters of these interactions are so chosen in such a way that they represent the long-range attraction and the short-range repulsion of the nucleon-nucleon interactions. These parameters are so chosen to reproduce good agreement between the calculated values of the binding energy, the root mean-square radius, the D-state probability, the magnetic dipole moment and the electric quadrupole moment of the deuteron nucleus. The variation method is then used to calculate the binding energy of triton by varying the oscillator parameter which exists in the nuclear wave function. The obtained nuclear wave functions are then used to calculate the root mean-square radius and the magnetic dipole moment of the triton.展开更多
The ability to navigate long distances is essential for many animals to locate shelter,food,and breeding grounds.Magnetic sense has evolved in various migratory and homing species to orient them based on the geomagnet...The ability to navigate long distances is essential for many animals to locate shelter,food,and breeding grounds.Magnetic sense has evolved in various migratory and homing species to orient them based on the geomagnetic field.A highly conserved ironsulfur cluster assembly protein IscA is proposed as an animal magnetoreceptor(MagR).Iron-sulfur cluster binding is also suggested to play an essential role in MagR magnetism and is thus critical in animal magnetoreception.In the current study,we provide evidence for distinct iron binding and iron-sulfur cluster binding in MagR in pigeons,an avian species that relies on the geomagnetic field for navigation and homing.Pigeon MagR showed significantly higher total iron content from both iron-and ironsulfur binding.Y65 in pigeon MagR was shown to directly mediate mononuclear iron binding,and its mutation abolished iron-binding capacity of the protein.Surprisingly,both iron binding and iron-sulfur binding demonstrated synergistic effects,and thus appear to be integral and indispensable to pigeon MagR magnetism.These results not only extend our current understanding of the origin and complexity of MagR magnetism,but also imply a possible molecular explanation for the huge diversity in animal magnetoreception.展开更多
After spinal cord injury(SCI),a fibroblast-and microglia-mediated fibrotic scar is formed in the lesion core,and a glial scar is formed around the fibrotic scar as a res ult of the activation and proliferation of astr...After spinal cord injury(SCI),a fibroblast-and microglia-mediated fibrotic scar is formed in the lesion core,and a glial scar is formed around the fibrotic scar as a res ult of the activation and proliferation of astrocytes.Simultaneously,a large number of neuro ns are lost in the injured area.Regulating the dense glial scar and re plenishing neurons in the injured area are essential for SCI repair.Polypyrimidine tra ct binding protein(PTB),known as an RNA-binding protein,plays a key role in neurogenesis.Here,we utilized short hairpin RNAs(shRNAs)and antisense oligonucleotides(ASOs)to knock down PTB expression.We found that reactive spinal astrocytes from mice were directly reprogrammed into motoneuron-like cells by PTB downregulation in vitro.In a mouse model of compressioninduced SCI,adeno-associated viral shRNA-mediated PTB knockdown replenished motoneuron-like cells around the injured area.Basso Mouse Scale scores and forced swim,inclined plate,cold allodynia,and hot plate tests showed that PTB knockdown promoted motor function recovery in mice but did not improve sensory perception after SCI.Furthermore,ASO-mediated PTB knockdown improved motor function resto ration by not only replenishing motoneuron-like cells around the injured area but also by modestly reducing the density of the glial scar without disrupting its overall structure.Together,these findings suggest that PTB knockdown may be a promising therapeutic strategy to promote motor function recovery during spinal cord repair.展开更多
Fidgetin,a microtubule-severing enzyme,regulates neurite outgrowth,axonal regeneration,and cell migration by trimming off the labile domain of microtubule polymers.Because maintenance of the microtubule labile domain ...Fidgetin,a microtubule-severing enzyme,regulates neurite outgrowth,axonal regeneration,and cell migration by trimming off the labile domain of microtubule polymers.Because maintenance of the microtubule labile domain is essential for axon initiation,elongation,and navigation,it is of interest to determine whether augmenting the microtubule labile domain via depletion of fidgetin serves as a therapeutic approach to promote axonal regrowth in spinal cord injury.In this study,we constructed rat models of spinal cord injury and sciatic nerve injury.Compared with spinal cord injury,we found that expression level of tyrosinated microtubules in the labile portion of microtubules continuously increased,whereas fidgetin decreased after peripheral nerve injury.Depletion of fidgetin enhanced axon regeneration after spinal cord injury,whereas expression level of end binding protein 3(EB3)markedly increased.Next,we performed RNA interference to knockdown EB3 or fidgetin.We found that deletion of EB3 did not change fidgetin expression.Conversely,deletion of fidgetin markedly increased expression of tyrosinated microtubules and EB3.Deletion of fidgetin increased the amount of EB3 at the end of neurites and thereby increased the level of tyrosinated microtubules.Finally,we deleted EB3 and overexpressed fidgetin.We found that fidgetin trimmed tyrosinated tubulins by interacting with EB3.When fidgetin was deleted,the labile portion of microtubules was elongated,and as a result the length of axons and number of axon branches were increased.These findings suggest that fidgetin can be used as a novel therapeutic target to promote axonal regeneration after spinal cord injury.Furthermore,they reveal an innovative mechanism by which fidgetin preferentially severs labile microtubules.展开更多
With the wide use of three-dimensional woven spacer composites(3DWSCs),the market expects greater mechanical properties from this material.By changing the weft fastening method of the traditional I-shape pile yarns,we...With the wide use of three-dimensional woven spacer composites(3DWSCs),the market expects greater mechanical properties from this material.By changing the weft fastening method of the traditional I-shape pile yarns,we designed three-dimensional woven spacer fabrics(3DWSFs)and 3DWSCs with the weft V-shape to improve the compression performance of traditional 3DWSFs.The effects of weft binding structures,V-pile densities,and V-shaped angle were investigated in this paper.It is found that the compression resistance of 3DWSFs with the weft V-shape is improved compared to that with the weft I-shape,the fabric height recovery rate is as high as 95.7%,and the average elastic recovery rate is 59.39%.When the interlayer pile yarn density is the same,the weft V-shaped and weft I-shaped 3DWSCs have similar flatwise pressure and edgewise pressure performance.The compression properties of the composite improve as the density of the V-pile yarns increases.The flatwise compression load decreases as the V-shaped angle decreases.When the V-shaped angle is 28°and 42°,the latitudinal V-shaped 3DWSCs perform exceptionally well in terms of anti-compression cushioning.The V-shaped weft binding method offers a novel approach to structural design of 3DWSCs.展开更多
Objective DUF538(domain of unknown function 538) domain containing proteins are known as putative hypothetical proteins in plants. Until yet, there is no much information regarding their structure and function. Method...Objective DUF538(domain of unknown function 538) domain containing proteins are known as putative hypothetical proteins in plants. Until yet, there is no much information regarding their structure and function. Methods In the present research work, the homologous structures and binding potentials were identified between plant/mammalian lipocalins and plant DUF538 protein by using bioinformatics and experimental tools including molecular dynamics simulation, molecular docking and recombinant technology-based techniques. Results Molecular docking analysis of their interactions with lipidic ligands including cholesterol and palmitic acid revealed the similar and comparable binding potentials between DUF538 and lipocalin proteins. Both the test proteins were found to have more affinity to cholesterol molecule in compare to palmitic acid. By using recombinant technology-based experiments, the heterologously expressed and purified fused product of DUF538 protein exhibited about 61% cholesterol binding ability. Conclusion As a conclusion, plants DUF538 protein family was predicted to be the structural and may be the functional homologues of plants/animals lipocalin superfamily.展开更多
Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in v...Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery.展开更多
The random forest algorithm was applied to study the nuclear binding energy and charge radius.The regularized root-mean-square of error(RMSE)was proposed to avoid overfitting during the training of random forest.RMSE ...The random forest algorithm was applied to study the nuclear binding energy and charge radius.The regularized root-mean-square of error(RMSE)was proposed to avoid overfitting during the training of random forest.RMSE for nuclides with Z,N>7 is reduced to 0.816 MeV and 0.0200 fm compared with the six-term liquid drop model and a three-term nuclear charge radius formula,respectively.Specific interest is in the possible(sub)shells among the superheavy region,which is important for searching for new elements and the island of stability.The significance of shell features estimated by the so-called shapely additive explanation method suggests(Z,N)=(92,142)and(98,156)as possible subshells indicated by the binding energy.Because the present observed data is far from the N=184 shell,which is suggested by mean-field investigations,its shell effect is not predicted based on present training.The significance analysis of the nuclear charge radius suggests Z=92 and N=136 as possible subshells.The effect is verified by the shell-corrected nuclear charge radius model.展开更多
基金The Guangdong Basic and Applied Basic Research Foundation(2022A1515010730)National Natural Science Foundation of China(32001647)+2 种基金National Natural Science Foundation of China(31972022)Financial and moral assistance supported by the Guangdong Basic and Applied Basic Research Foundation(2019A1515011996)111 Project(B17018)。
文摘In this study,the structural characters,antioxidant activities and bile acid-binding ability of sea buckthorn polysaccharides(HRPs)obtained by the commonly used hot water(HRP-W),pressurized hot water(HRP-H),ultrasonic(HRP-U),acid(HRP-C)and alkali(HRP-A)assisted extraction methods were investigated.The results demonstrated that extraction methods had significant effects on extraction yield,monosaccharide composition,molecular weight,particle size,triple-helical structure,and surface morphology of HRPs except for the major linkage bands.Thermogravimetric analysis showed that HRP-U with filamentous reticular microstructure exhibited better thermal stability.The HRP-A with the lowest molecular weight and highest arabinose content possessed the best antioxidant activities.Moreover,the rheological analysis indicated that HRPs with higher galacturonic acid content and molecular weight showed higher viscosity and stronger crosslinking network(HRP-C,HRP-W and HRP-U),which exhibited stronger bile acid binding capacity.The present findings provide scientific evidence in the preparation technology of sea buckthorn polysaccharides with good antioxidant and bile acid binding capacity which are related to the structure affected by the extraction methods.
文摘Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.
基金the National Key R&D Program of China(No.2023YFA1606503)the National Natural Science Foundation of China(Nos.12035011,11975167,11947211,11905103,11881240623,and 11961141003).
文摘Reliable calculations of nuclear binding energies are crucial for advancing the research of nuclear physics. Machine learning provides an innovative approach to exploring complex physical problems. In this study, the nuclear binding energies are modeled directly using a machine-learning method called the Gaussian process. First, the binding energies for 2238 nuclei with Z > 20 and N > 20 are calculated using the Gaussian process in a physically motivated feature space, yielding an average deviation of 0.046 MeV and a standard deviation of 0.066 MeV. The results show the good learning ability of the Gaussian process in the studies of binding energies. Then, the predictive power of the Gaussian process is studied by calculating the binding energies for 108 nuclei newly included in AME2020. The theoretical results are in good agreement with the experimental data, reflecting the good predictive power of the Gaussian process. Moreover, the α-decay energies for 1169 nuclei with 50 ≤ Z ≤ 110 are derived from the theoretical binding energies calculated using the Gaussian process. The average deviation and the standard deviation are, respectively, 0.047 MeV and 0.070 MeV. Noticeably, the calculated α-decay energies for the two new isotopes ^ (204 )Ac(Huang et al. Phys Lett B 834, 137484(2022)) and ^ (207) Th(Yang et al. Phys Rev C 105, L051302(2022)) agree well with the latest experimental data. These results demonstrate that the Gaussian process is reliable for the calculations of nuclear binding energies. Finally, the α-decay properties of some unknown actinide nuclei are predicted using the Gaussian process. The predicted results can be useful guides for future research on binding energies and α-decay properties.
基金the Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province,China(Grant No.2022SDZG05)the National Natural Science Foundation of China(Grants Nos.32000457,31871231,and 31921004)+1 种基金the Major Program of Guangdong Basic and Applied Research,China(Grant No.2019B030302006)the Double First-Class Discipline Promotion Project,China(Grant No.2021B10564001).
文摘Pentatricopeptide repeat(PPR)proteins represent one of the largest protein families in plants and typically localize to organelles like mitochondria and chloroplasts.By contrast,CYTOPLASMLOCALIZED PPR1(OsCPPR1)is a cytoplasm-localized PPR protein that can degrade OsGOLDENLIKE1(OsGLK1)mRNA in the tapetum of rice anther.However,the mechanism,by which OsCPPR1 recognizes and binds to OsGLK1 transcripts,remains unknown.Through protein structure prediction and macromolecular docking experiments,we observed that distinct PPR motif structures of OsCPPR1 exhibited varying binding efficiencies to OsGLK1 RNA.Moreover,RNA-electrophoretic mobility shift assay experiment demonstrated that the recombinant OsCPPR1 can directly recognize and bind to OsGLK1 mRNA in vitro.This further confirmed that the mutations in the conserved amino acids in each PPR motif resulted in loss of activity,while truncation of OsCPPR1 decreased its binding efficiency.These findings collectively suggest that it may require some co-factors to assist in cleavage,a facet that warrants further exploration in subsequent studies.
基金sopported by National Natural Science Foundation of China(31960457)Jiangxi Province National Science and Technology Prizes Backup Project and Cultivation Plan(20212AEI91001).
文摘Gut microbiota plays an important role in food allergy.The immunoglobulin G(IgG)/immunoglobulin E(IgE)binding capacity and human gut microbiota changes of digestion products derived from glycated ovalbumin(OVA)were investigated.Gastrointestinal digestion effectively destroyed the primary structure of glycated OVA,resulting in a significantly higher digestibility than gastric digestion,and more abundant peptides<3 kDa.Moreover,gastric and gastrointestinal digestion products have different fluorescence quenching and red shift of fluorescence peaks,and possess different conformational structures.These changes resulted in a decrease in 28.7%of the IgE binding capacity of gastrointestinal digestion products beyond that of pepsin.Moreover,gastrointestinal digestion products of glycated OVA increased significantly the proportion of Subdoligranulum,Collinsella,and Bifidobacterium.Therefore,gastrointestinal digestion products of glycated OVA altered human intestinal microbiota,reducing the risk of potential allergy.
基金Supported by the National Natural Science Foundation of China,No.82272996the Science and Technology Program of Guangzhou,No.202206010081.
文摘Colorectal cancer(CRC)ranks third in the number of cancers mainly because of the inability to diagnose it at an early stage.The pathogenesis of CRC is complicated,which is the result of the complex interaction of multiple genetic and environmental factors.Currently,one of the main treatments for CRC is chemotherapy.But the primary cause of CRC treatment failure is drug resistance.The expression of cyclin-dependent kinase 9(CDK9)was correlated with elevated autophagy levels in colon cancer,and high expression of CDK9 indicates a poor prognosis in CRC.The incidence of autophagy and the expressions of Beclin 1 and ATP binding cassette transporter G2 are different in left and right colon cancer,and autophagy may be involved in the occurrence of chemotherapy resistance.In this article,the roles of CDK9,ATP binding cassette transporter G2 and Beclin 1 in CRC were elucidated,emphasizing the linkages among them and providing potential therapeutic targets of CRC.
基金pported by the Natural Science Foundation of Inner Mongolia Autonomous Region,No.2022MS08057.
文摘BACKGROUND The intricate relationship between type 2 diabetes mellitus(T2DM)and diabetic nephropathy(DN)presents a challenge in understanding the significance of various biomarkers in diagnosis.AIM To elucidate the roles and diagnostic values ofα2-macroglobulin(α2-MG),podocalyxin(PCX),α-L-fucosidase(AFU),retinol-binding protein-4(RBP-4),and cystatin C(CysC)in DN.METHODS From December 2018 to December 2020,203 T2DM patients were enrolled in the study.Of these,115 were diagnosed with DN(115 patients),while the remaining 88 patients were classified as non-DN.The urinary levels ofα2-MG,PCX,and AFU and the serum concentrations RBP-4 and CysC were measured in conjunction with other relevant clinical indicators to evaluate their potential correlations and diagnostic utility.RESULTS After adjustments for age and gender,significant positive correlations were observed between the biomarkers CysC,RBP-4,α2-MG/urinary creatinine(UCr),PCX/UCr,and AFU/UCr,and clinical indicators such as urinary albumin-to-creatinine ratio(UACR),serum creatinine,urea,24-h total urine protein,and neutrophil-to-lymphocyte ratio(NLR).Conversely,these biomarkers exhibited negative correlations with the estimated glomerular filtration rate(P<0.05).Receiver operating characteristic(ROC)curve analysis further demonstrated the diagnostic performance of these biomarkers,with UACR showcasing the highest area under the ROC curve(AUC^(ROC))at 0.97.CONCLUSION This study underscores the diagnostic significance ofα2-MG,PCX,and AFU in the development of DN.The biomarkers RBP-4,CysC,PCX,AFU,andα2-MG provide promising diagnostic insights,while UACR is the most potent diagnostic biomarker in assessing DN.
基金Tianjin Key Medical Discipline Construction Project,No.TJYXZDXK-034A.
文摘BACKGROUND Hepatocellular carcinoma(HCC)is an aggressive subtype of liver cancer and is one of the most common cancers with high mortality worldwide.Reprogrammed lipid metabolism plays crucial roles in HCC cancer cell survival,growth,and evolution.Emerging evidence suggests the importance of fatty acid binding proteins(FABPs)in contribution to cancer progression and metastasis;however,how these FABPs are dysregulated in cancer cells,especially in HCC,and the roles of FABPs in cancer progression have not been well defined.AIM To understand the genetic alterations and expression of FABPs and their associated cancer hallmarks and oncogenes in contributing to cancer malignancies.METHODS We used The Cancer Genome Atlas datasets of pan cancer and liver hepatocellular carcinoma(LIHC)as well as patient cohorts with other cancer types in this study.We investigated genetic alterations of FABPs in various cancer types.mRNA expression was used to determine if FABPs are abnormally expressed in tumor tissues compared to non-tumor controls and to investigate whether their expression correlates with patient clinical outcome,enriched cancer hallmarks and oncogenes previously reported for patients with HCC.We determined the protein levels of FABP5 and its correlated genes in two HCC cell lines and assessed the potential of FABP5 inhibition in treating HCC cells.RESULTS We discovered that a gene cluster including five FABP family members(FABP4,FABP5,FABP8,FABP9 and FABP12)is frequently co-amplified in cancer.Amplification,in fact,is the most common genetic alteration for FABPs,leading to overexpression of FABPs.FABP5 showed the greatest differential mRNA expression comparing tumor with non-tumor tissues.High FABP5 expression correlates well with worse patient outcomes(P<0.05).FABP5 expression highly correlates with enrichment of G2M checkpoint(r=0.33,P=1.1e-10),TP53 signaling pathway(r=0.22,P=1.7e-5)and many genes in the gene sets such as CDK1(r=0.56,P=0),CDK4(r=0.49,P=0),and TP53(r=0.22,P=1.6e-5).Furthermore,FABP5 also correlates well with two co-expressed oncogenes PLK1 and BIRC5 in pan cancer especially in LIHC patients(r=0.58,P=0;r=0.58,P=0;respectively).FABP5high Huh7 cells also expressed higher protein levels of p53,BIRC5,CDK1,CDK2,and CDK4 than FABP5low HepG2 cells.FABP5 inhibition more potently inhibited the tumor cell growth in Huh7 cells than in HepG2 cells.CONCLUSION We discovered that FABP5 gene is frequently amplified in cancer,especially in HCC,leading to its significant elevated expression in HCC.Its high expression correlates well with worse patient outcome,enriched cancer hallmarks and oncogenes in HCC.FABP5 inhibition impaired the cell viability of FABP5high Huh7 cells.All these support that FABP5 is a novel therapeutic target for treating FABP5high HCC.
基金Supported by General Program of National Natural Science Foundation of China,No.81770197Scientific and Technological Research Major Program of Chongqing Municipal Education Commission,No.KJZD-M202312802+1 种基金Chongqing Natural Science Foundation of China,No.CSTB2022NSCQ-MSX0190,No.CSTB2022NSCQ-MSX0176,and No.cstc2020jcyj-msxmX0051Xinqiao Young Postdoc Talent Incubation Program,No.2022YQB098.
文摘BACKGROUND Thrombocytopenia 2,an autosomal dominant inherited disease characterized by moderate thrombocytopenia,predisposition to myeloid malignancies and normal platelet size and function,can be caused by 5’-untranslated region(UTR)point mutations in ankyrin repeat domain containing 26(ANKRD26).Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1)have been identified as negative regulators of ANKRD26.However,the positive regulators of ANKRD26 are still unknown.AIM To prove the positive regulatory effect of GATA binding protein 2(GATA2)on ANKRD26 transcription.METHODS Human induced pluripotent stem cells derived from bone marrow(hiPSC-BM)INTRODUCTION Ankyrin repeat domain containing protein 26(ANKRD26)acts as a regulator of adipogenesis and is involved in the regulation of feeding behavior[1-3].The ANKRD26 gene is located on chromosome 10 and shares regions of homology with the primate-specific gene family POTE.According to the Human Protein Atlas database,the ANKRD26 protein is localized to the Golgi apparatus and vesicles,and its expression can be detected in nearly all human tissues[4].Moreover,UniProt annotation revealed that ANKRD26 is localized in the centrosome and contains coiled-coil domains formed by spectrin helices and ankyrin repeats[5,6].The most common disease related to ANKRD26 is thrombocytopenia 2(THC2),which is a rare autosomal dominant inherited disease characterized by lifelong mild-to-moderate thrombocytopenia and mild bleeding[7-9].Caused by the variants in the 5’-untranslated region(UTR)of ANKRD26,THC2 is defined by a decrease in the number of platelets in circulating blood and results in increased bleeding and decreased clotting ability[8,10].Due to the point mutations that occur in the 5’-UTR of ANKRD26,its negative transcription factors(TFs),Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1),lose their repression effect[11].The persistent expression of ANKRD26 increases the activity of the mitogen activated protein kinase and extracellular signal regulated kinase 1/2 signaling pathways,which are potentially involved in the regulation of thrombopoietin-dependent signaling and further impair proplatelet formation by megakaryocytes(MKs)[11].However,the positive regulators of ANKRD26,which might be associated with THC2 pathology,are still unknown.
文摘Hydrophobic Val derivative Schiff base copper(II) complexes and dipeptide (AlaAla, GlyGly) derivative Schiff base copper(II) complexes were introduced into egg white lysozyme. X-ray crystal structure analysis revealed amino acid derivative Schiff base copper(II) complexes were obtained. Herein we discuss primarily on the binding mode of copper(II) of the complexes obtained with egg white lysozyme. The electron density of copper(II) ions was confirmed by X-ray crystal structure analysis. The Val derivative Schiff base copper(II) complex was weakly bound at Arg114 of egg white lysozyme. In other copper(II) complexes, binding of copper(II) ions with dissociated ligands to various residues was observed. The binding sites of copper(II) ions were compared with computational scientific predictions.
基金Supported by Guangxi Zhuang Autonomous Region Health Commission Scientific Research Project,No.Z-A20220415 and No.Z20210442The First Affiliated Hospital of Guangxi Medical University Provincial and Ministerial Key Laboratory Cultivation Project:Guangxi Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer,No.21-220-18.
文摘BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetically targeting some genes.Our study will examine the expression,potential effect,biological function and clinical value of SYNCRIP in CRC.AIM To examine the expression,potential effect,biological function and clinical value METHODS The expression of SYNCRIP was examined by immunohistochemistry arrays and high-throughput data.The effect of SYNCRIP gene in CRC cell growth was evaluated by CRISPR-Cas9 technology.The target genes of SYNCRIP were calculated using various algorithms,and the molecular mechanism of SYNCRIP in CRC was explored by mutation analysis and pathway analysis.The clinical value of SYNCRIP in prognosis and radiotherapy was revealed via evidence-based medicine methods.RESULTS The protein and mRNA levels of SYNCRIP were both highly expressed in CRC samples compared to nontumorous tissue based on 330 immunohistochemistry arrays and 3640 CRC samples.Cells grew more slowly in eleven CRC cell lines after knocking out the SYNCRIP gene.SYNCRIP could epigenetically target genes to promote the occurrence and development of CRC by boosting the cell cycle and affecting the tumor microenvironment.In addition,CRC patients with high SYNCRIP expression are more sensitive to radiotherapy.CONCLUSION SYNCRIP is upregulated in CRC,and highly expressed SYNCRIP can accelerate CRC cell division by exerting its epigenetic regulatory effects.In addition,SYNCRIP is expected to become a potential biomarker to predict the effect of radiotherapy.
文摘In this paper, we consider the relationship between the binding number and the existence of fractional k-factors of graphs. The binding number of G is defined by Woodall as bind(G)=min{ | NG(X) || X |:∅≠X⊆V(G) }. It is proved that a graph G has a fractional 1-factor if bind(G)≥1and has a fractional k-factor if bind(G)≥k−1k. Furthermore, it is showed that both results are best possible in some sense.
文摘The basis functions of the translation invariant shell model are used to construct the ground state nuclear wave functions of <sup>3</sup>H. The used residual two-body interactions consist of central, tensor, spin orbit and quadratic spin orbit terms with Gaussian radial dependence. The parameters of these interactions are so chosen in such a way that they represent the long-range attraction and the short-range repulsion of the nucleon-nucleon interactions. These parameters are so chosen to reproduce good agreement between the calculated values of the binding energy, the root mean-square radius, the D-state probability, the magnetic dipole moment and the electric quadrupole moment of the deuteron nucleus. The variation method is then used to calculate the binding energy of triton by varying the oscillator parameter which exists in the nuclear wave function. The obtained nuclear wave functions are then used to calculate the root mean-square radius and the magnetic dipole moment of the triton.
基金supported by the National Natural Science Foundation of China(31640001 to C.X.,U21A20148 to X.Z.and C.X.)the Presidential Foundation of Hefei Institutes of Physical Science,Chinese Academy of Sciences(Y96XC11131,E26CCG27,and E26CCD15 to C.X.)。
文摘The ability to navigate long distances is essential for many animals to locate shelter,food,and breeding grounds.Magnetic sense has evolved in various migratory and homing species to orient them based on the geomagnetic field.A highly conserved ironsulfur cluster assembly protein IscA is proposed as an animal magnetoreceptor(MagR).Iron-sulfur cluster binding is also suggested to play an essential role in MagR magnetism and is thus critical in animal magnetoreception.In the current study,we provide evidence for distinct iron binding and iron-sulfur cluster binding in MagR in pigeons,an avian species that relies on the geomagnetic field for navigation and homing.Pigeon MagR showed significantly higher total iron content from both iron-and ironsulfur binding.Y65 in pigeon MagR was shown to directly mediate mononuclear iron binding,and its mutation abolished iron-binding capacity of the protein.Surprisingly,both iron binding and iron-sulfur binding demonstrated synergistic effects,and thus appear to be integral and indispensable to pigeon MagR magnetism.These results not only extend our current understanding of the origin and complexity of MagR magnetism,but also imply a possible molecular explanation for the huge diversity in animal magnetoreception.
基金supported by the National Natural Science Foundation of China,Nos.82101455(to RYY),31872773(to GC),82001168(to JYP)the Key Research and Development Program(Social Development)of Jiangsu Province,No.BE2020667(to GC)+3 种基金the Foundation of Jiangsu Province,333 Project High-level Talents",No.BRA2020076(to GC)the Nantong Civic Science and Technology Project of China,No.JC2020028(to RYY)the Natural Science Research of Jiangsu Higher Education Institutions of China,No.19KJB310012(to RYY)Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)。
文摘After spinal cord injury(SCI),a fibroblast-and microglia-mediated fibrotic scar is formed in the lesion core,and a glial scar is formed around the fibrotic scar as a res ult of the activation and proliferation of astrocytes.Simultaneously,a large number of neuro ns are lost in the injured area.Regulating the dense glial scar and re plenishing neurons in the injured area are essential for SCI repair.Polypyrimidine tra ct binding protein(PTB),known as an RNA-binding protein,plays a key role in neurogenesis.Here,we utilized short hairpin RNAs(shRNAs)and antisense oligonucleotides(ASOs)to knock down PTB expression.We found that reactive spinal astrocytes from mice were directly reprogrammed into motoneuron-like cells by PTB downregulation in vitro.In a mouse model of compressioninduced SCI,adeno-associated viral shRNA-mediated PTB knockdown replenished motoneuron-like cells around the injured area.Basso Mouse Scale scores and forced swim,inclined plate,cold allodynia,and hot plate tests showed that PTB knockdown promoted motor function recovery in mice but did not improve sensory perception after SCI.Furthermore,ASO-mediated PTB knockdown improved motor function resto ration by not only replenishing motoneuron-like cells around the injured area but also by modestly reducing the density of the glial scar without disrupting its overall structure.Together,these findings suggest that PTB knockdown may be a promising therapeutic strategy to promote motor function recovery during spinal cord repair.
基金the National Natural Science Foundation of China,Nos.32070725(to ML),82001295(to RHW),31970412(to YL)the Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutions。
文摘Fidgetin,a microtubule-severing enzyme,regulates neurite outgrowth,axonal regeneration,and cell migration by trimming off the labile domain of microtubule polymers.Because maintenance of the microtubule labile domain is essential for axon initiation,elongation,and navigation,it is of interest to determine whether augmenting the microtubule labile domain via depletion of fidgetin serves as a therapeutic approach to promote axonal regrowth in spinal cord injury.In this study,we constructed rat models of spinal cord injury and sciatic nerve injury.Compared with spinal cord injury,we found that expression level of tyrosinated microtubules in the labile portion of microtubules continuously increased,whereas fidgetin decreased after peripheral nerve injury.Depletion of fidgetin enhanced axon regeneration after spinal cord injury,whereas expression level of end binding protein 3(EB3)markedly increased.Next,we performed RNA interference to knockdown EB3 or fidgetin.We found that deletion of EB3 did not change fidgetin expression.Conversely,deletion of fidgetin markedly increased expression of tyrosinated microtubules and EB3.Deletion of fidgetin increased the amount of EB3 at the end of neurites and thereby increased the level of tyrosinated microtubules.Finally,we deleted EB3 and overexpressed fidgetin.We found that fidgetin trimmed tyrosinated tubulins by interacting with EB3.When fidgetin was deleted,the labile portion of microtubules was elongated,and as a result the length of axons and number of axon branches were increased.These findings suggest that fidgetin can be used as a novel therapeutic target to promote axonal regeneration after spinal cord injury.Furthermore,they reveal an innovative mechanism by which fidgetin preferentially severs labile microtubules.
基金Fundamental Research Funds for the Central Universities,China(Nos.2232022D-11 and 22D128102/007)Jiangsu Transformation and Upgrading Funding Program for Industrial and Information Industry,ChinaShanghai Natural Science Foundation of Shanghai Municipal Science and Technology Commission,China(No.20ZR1401600)。
文摘With the wide use of three-dimensional woven spacer composites(3DWSCs),the market expects greater mechanical properties from this material.By changing the weft fastening method of the traditional I-shape pile yarns,we designed three-dimensional woven spacer fabrics(3DWSFs)and 3DWSCs with the weft V-shape to improve the compression performance of traditional 3DWSFs.The effects of weft binding structures,V-pile densities,and V-shaped angle were investigated in this paper.It is found that the compression resistance of 3DWSFs with the weft V-shape is improved compared to that with the weft I-shape,the fabric height recovery rate is as high as 95.7%,and the average elastic recovery rate is 59.39%.When the interlayer pile yarn density is the same,the weft V-shaped and weft I-shaped 3DWSCs have similar flatwise pressure and edgewise pressure performance.The compression properties of the composite improve as the density of the V-pile yarns increases.The flatwise compression load decreases as the V-shaped angle decreases.When the V-shaped angle is 28°and 42°,the latitudinal V-shaped 3DWSCs perform exceptionally well in terms of anti-compression cushioning.The V-shaped weft binding method offers a novel approach to structural design of 3DWSCs.
基金supported by a grant from Department of Animal Biology and Research Center for Bioscience and Biotechnology(RCBB),University of Tabriz(6906).
文摘Objective DUF538(domain of unknown function 538) domain containing proteins are known as putative hypothetical proteins in plants. Until yet, there is no much information regarding their structure and function. Methods In the present research work, the homologous structures and binding potentials were identified between plant/mammalian lipocalins and plant DUF538 protein by using bioinformatics and experimental tools including molecular dynamics simulation, molecular docking and recombinant technology-based techniques. Results Molecular docking analysis of their interactions with lipidic ligands including cholesterol and palmitic acid revealed the similar and comparable binding potentials between DUF538 and lipocalin proteins. Both the test proteins were found to have more affinity to cholesterol molecule in compare to palmitic acid. By using recombinant technology-based experiments, the heterologously expressed and purified fused product of DUF538 protein exhibited about 61% cholesterol binding ability. Conclusion As a conclusion, plants DUF538 protein family was predicted to be the structural and may be the functional homologues of plants/animals lipocalin superfamily.
文摘Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery.
基金Supported by Basic and Applied Basic Research Project of Guangdong Province(2021B0301030006)。
文摘The random forest algorithm was applied to study the nuclear binding energy and charge radius.The regularized root-mean-square of error(RMSE)was proposed to avoid overfitting during the training of random forest.RMSE for nuclides with Z,N>7 is reduced to 0.816 MeV and 0.0200 fm compared with the six-term liquid drop model and a three-term nuclear charge radius formula,respectively.Specific interest is in the possible(sub)shells among the superheavy region,which is important for searching for new elements and the island of stability.The significance of shell features estimated by the so-called shapely additive explanation method suggests(Z,N)=(92,142)and(98,156)as possible subshells indicated by the binding energy.Because the present observed data is far from the N=184 shell,which is suggested by mean-field investigations,its shell effect is not predicted based on present training.The significance analysis of the nuclear charge radius suggests Z=92 and N=136 as possible subshells.The effect is verified by the shell-corrected nuclear charge radius model.
