The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co...The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.展开更多
Gut microbiota play important roles in the immunity,digestion,and energy meta bolism of their reptile hosts.Mangshan pit viper(Protobothrops mangshanensis)is a critically endangered snake species that is a Class I nat...Gut microbiota play important roles in the immunity,digestion,and energy meta bolism of their reptile hosts.Mangshan pit viper(Protobothrops mangshanensis)is a critically endangered snake species that is a Class I national protected species in China.Little is known regarding the relationship between P.mangshanensis and their gut microbial communities.In this study,the gut microbiota of wild P.mangshanensis individuals,artificially hiberna ting captive individuals,and non-hibernating captive individuals were compared across nine samples.Comparative shotgun metagenomic analysis was used to investigate the taxonomic composition,diversity,and function of P.mangshanensis gut microbial communities and assess whether their gut microbiomes were affected by their living environments and captivity conditions.The dominant phyla within P.mangshanensis gut microbial communities were Proteobacteria(65.55%),Bacteroidetes(15.97%),and Firmicutes(8.11%).Enriched functional pathways within the gut microbiota included meta bolism(54.9%),environmental information processing(9.67%),and genetic information processing(9.37%).Wild snake gut communities exhibited higher microbial diversity than the other two groups.The gut microbiomes of wild and hibernating captive snakes may be more reflective of healthy intestinal homeostasis than that in nonhibernating snakes.Specifically,non-hibernating snakes exhibited increased levelsof potentially pathogenic populations and functional specialization within gut microbial communities.Thus,different livingenvironments and captivitymethodsmay correspond to major shifts in microbiota composition,diversity,and function within P.mangshanensis.This study provides important insights to help guide the conservation of P.mangshanensis,while also carrying broad implications for our understanding of the effects of living environments and non-hibernating captivity conditions on the gut microbiota of snakes.展开更多
Density functional theory was employed to study the dehydration mechanism of MgCI_2·4H_2O. Analysis of potential energy surface（PES） of possible pathways indicated that the most possible way was one of the wate...Density functional theory was employed to study the dehydration mechanism of MgCI_2·4H_2O. Analysis of potential energy surface（PES） of possible pathways indicated that the most possible way was one of the water molecules halfly dissociated with an elongated bond distance with Mg^2＋,where electrostatic interaction played a leading role; another water molecule dissociated sequentially. It was in agreement with the result from differencial thermal analysis. The dehydration process of MgCI_2·4H_2O was clarified theoretically,promoting the theoretical study of dehydration of MgCI_2·2H_2O.展开更多
Electroacupuncture is beneficial for the recovery of spinal cord injury, but the underlying mechanism is unclear. The Rho/Rho-associated kinase（ROCK） signaling pathway regulates the actin cytoskeleton by controlling...Electroacupuncture is beneficial for the recovery of spinal cord injury, but the underlying mechanism is unclear. The Rho/Rho-associated kinase（ROCK） signaling pathway regulates the actin cytoskeleton by controlling the adhesive and migratory behaviors of cells that could inhibit neurite regrowth after neural injury and consequently hinder the recovery from spinal cord injury. Therefore, we hypothesized electroacupuncture could affect the Rho/ROCK signaling pathway to promote the recovery of spinal cord injury. In our experiments, the spinal cord injury in adult Sprague-Dawley rats was caused by an impact device. Those rats were subjected to electroacupuncture at Yaoyangguan（GV3）, Dazhui（GV14）, Zusanli（ST36） and Ciliao（BL32） and/or monosialoganglioside treatment. Behavioral scores revealed that the hindlimb motor functions improved with those treatments. Real-time quantitative polymerase chain reaction, fluorescence in situ hybridization and western blot assay showed that electroacupuncture suppressed the m RNA and protein expression of Rho-A and Rho-associated kinase Ⅱ（ROCKⅡ） of injured spinal cord. Although monosialoganglioside promoted the recovery of hindlimb motor function, monosialoganglioside did not affect the expression of Rho-A and ROCKⅡ. However, electroacupuncture combined with monosialoganglioside did not further improve the motor function or suppress the expression of Rho-A and ROCKⅡ. Our data suggested that the electroacupuncture could specifically inhibit the activation of the Rho/ROCK signaling pathway thus partially contributing to the repair of injured spinal cord. Monosialoganglioside could promote the motor function but did not suppress expression of Rho A and ROCKⅡ. There was no synergistic effect of electroacupuncture combined with monosialoganglioside.展开更多
Propose:To investigate the molecular mechanisms underlying the protective effects of ischemic pre-conditioning(IPC)in patients undergoing total knee arthroplasty.Methods:GSE21164 was extracted from an online database,...Propose:To investigate the molecular mechanisms underlying the protective effects of ischemic pre-conditioning(IPC)in patients undergoing total knee arthroplasty.Methods:GSE21164 was extracted from an online database,followed by an investigation of differentiallyexpressed genes(DEGs)between IPC treatment samples at 2 time points(T0T and T1T).Function andpathway enrichment analyses were performed on the DEGs.A protein-protein interaction network wasconstructed to identify hub genes according to 5 different algorithms,followed by enrichment analysis.In addition,long noncoding RNAs(lncRNAs)were identified between the T0T and T1T samples.Furthermore,a competing endogenous RNA network was predicted based on the identified lncRNA-messenger RNA(mRNA),lncRNA-microRNA(miRNA),and mRNA-miRNA relationships revealed in thisstudy.Finally,a drug-gene network was investigated.Statistical analyses were performed usingGraphPad Prism 8.0.Differences between groups were determined using an unpaired t-test.p<0.05 wasconsidered significant.Results:A total of 343 DEGs at T0 and 10 DEGs at T1 were identified and compared with their respectivecontrol groups,followed by 100 DEGs between T0T and T1T.Based on these 100 DEGs,protein-proteininteraction network analysis revealed 9 hub genes,mainly with mitochondria-related functions andthe carbon metabolism pathway.Six differentially expressed lncRNAs were investigated between T0T andT1T.A competing endogenous RNA network was constructed using 259 lncRNAemiRNAemRNA in-teractions,including alpha-2-macroglobulin antisense RNA 1-miR-7161-5p-iron-sulfur cluster scaffold.Finally,13 chemical drugs associated with the hub genes were explored.Conclusion:Iron-sulfur cluster scaffold may promote IPC-induced ischemic tolerance mediated by alpha-2-macroglobulin antisense RNA 1-miR-7161-5p axis.Moreover,IPC may induce a protective responseafter total knee arthroplasty via mitochondria-related functions and the carbon metabolism pathway,which should be further validated in the near future.展开更多
Background Persistence of slow pathway (SP) function after SP modification is not uncommon after successful rediofrequency (RF) ablation of typical AV nodal reentry tachycardia (AVNRT). Methods and results We compa...Background Persistence of slow pathway (SP) function after SP modification is not uncommon after successful rediofrequency (RF) ablation of typical AV nodal reentry tachycardia (AVNRT). Methods and results We compared two methods (maximal AH interval during decremental atrial stimlation vs occurrence of AV nodal echos or dual AV nodal physiology (DAVNP): ≥50 msec increment in AH interval with a 10 msec decrement in A1A2) for the assessment of SP function immediately and 40 minutes after successful RF modification of SP. In 31 consecutive patients (age: 51±16 years, 18 women, 13 men) with typical AVNRT, SP modification was performed using a combined anatomic and electrogram guided approach. Immediately after successful SP modification, AV nodal function was assessed. This was repeated 40 minutes later. RF modification of SP was successful in all 31 patients. There was no recurrance during a 5±3 month follow up period. There was no significant difference between the electrophysiological parameters immediately and University of Frankfurt, Germany (Li YG, Bogun F, Grnefeld G, Hohnloser SH and Goethe JW)40 min after successful SP modification. There was evidence of SP function in 14 patients (6 with DAVNP+AV nodal echoes, 8 with either DAVNP or AV nodal echos) immehiately after SP modification. These patients could be differentiated from the patients without remaining SP function by maximal AH interval (298±102 msec vs 198±72 msec, P=0.004). 40 minutes after the suucessful SP modification, 11 patients displayed SP function (4 patients with DAVNP+AV nodal echos, 7 patients with either DAVNP or AV nodal echos). These patients could also be differentiated from the remaining patients with the use of the maximal AH interval (294±89 msec vs 189±50 msec, P<0.001).[BHDFG3,WK9ZQ,WK6,WK10*2,WK5W]Befroe SP modificationImmediately after RF40 min after RF[BHDZG1*2,WK9ZQ,WK6,WK10*2,WK5W]AVNERP (msec)258±44310±116316±114AVBCL (msec)330±55384±113376±110VABCL (msec)306±67306± 66311±54Max AH (msec)337±96247±100233±86 Conclusion SP function assessed immediately and 40 minutes after a successful SP modification remains stable. SP function can be assessed reliable by maximal AH interval during decremental atrial stimulation.展开更多
基金Supported by Shanghai Municipal Education Committee Educationand Scientific Research (Grant No. 07ZZ60)~~
文摘The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.
基金supported by the National Natural Science Foundation of China (Grant No. 31472021)the Project for Wildlife Conservation and Management of the National Forestry and Grassland Administration of China (Grant No. 2021-HN-001)the Wildlife Conservation Project of Hunan Province (Grant No. HNYB2019-001)
文摘Gut microbiota play important roles in the immunity,digestion,and energy meta bolism of their reptile hosts.Mangshan pit viper(Protobothrops mangshanensis)is a critically endangered snake species that is a Class I national protected species in China.Little is known regarding the relationship between P.mangshanensis and their gut microbial communities.In this study,the gut microbiota of wild P.mangshanensis individuals,artificially hiberna ting captive individuals,and non-hibernating captive individuals were compared across nine samples.Comparative shotgun metagenomic analysis was used to investigate the taxonomic composition,diversity,and function of P.mangshanensis gut microbial communities and assess whether their gut microbiomes were affected by their living environments and captivity conditions.The dominant phyla within P.mangshanensis gut microbial communities were Proteobacteria(65.55%),Bacteroidetes(15.97%),and Firmicutes(8.11%).Enriched functional pathways within the gut microbiota included meta bolism(54.9%),environmental information processing(9.67%),and genetic information processing(9.37%).Wild snake gut communities exhibited higher microbial diversity than the other two groups.The gut microbiomes of wild and hibernating captive snakes may be more reflective of healthy intestinal homeostasis than that in nonhibernating snakes.Specifically,non-hibernating snakes exhibited increased levelsof potentially pathogenic populations and functional specialization within gut microbial communities.Thus,different livingenvironments and captivitymethodsmay correspond to major shifts in microbiota composition,diversity,and function within P.mangshanensis.This study provides important insights to help guide the conservation of P.mangshanensis,while also carrying broad implications for our understanding of the effects of living environments and non-hibernating captivity conditions on the gut microbiota of snakes.
基金supported by the National Natural Science Foundation of China(No.21361021)
文摘Density functional theory was employed to study the dehydration mechanism of MgCI_2·4H_2O. Analysis of potential energy surface（PES） of possible pathways indicated that the most possible way was one of the water molecules halfly dissociated with an elongated bond distance with Mg^2＋,where electrostatic interaction played a leading role; another water molecule dissociated sequentially. It was in agreement with the result from differencial thermal analysis. The dehydration process of MgCI_2·4H_2O was clarified theoretically,promoting the theoretical study of dehydration of MgCI_2·2H_2O.
基金supported by the National Natural Science Foundation of China,No.81360562
文摘Electroacupuncture is beneficial for the recovery of spinal cord injury, but the underlying mechanism is unclear. The Rho/Rho-associated kinase（ROCK） signaling pathway regulates the actin cytoskeleton by controlling the adhesive and migratory behaviors of cells that could inhibit neurite regrowth after neural injury and consequently hinder the recovery from spinal cord injury. Therefore, we hypothesized electroacupuncture could affect the Rho/ROCK signaling pathway to promote the recovery of spinal cord injury. In our experiments, the spinal cord injury in adult Sprague-Dawley rats was caused by an impact device. Those rats were subjected to electroacupuncture at Yaoyangguan（GV3）, Dazhui（GV14）, Zusanli（ST36） and Ciliao（BL32） and/or monosialoganglioside treatment. Behavioral scores revealed that the hindlimb motor functions improved with those treatments. Real-time quantitative polymerase chain reaction, fluorescence in situ hybridization and western blot assay showed that electroacupuncture suppressed the m RNA and protein expression of Rho-A and Rho-associated kinase Ⅱ（ROCKⅡ） of injured spinal cord. Although monosialoganglioside promoted the recovery of hindlimb motor function, monosialoganglioside did not affect the expression of Rho-A and ROCKⅡ. However, electroacupuncture combined with monosialoganglioside did not further improve the motor function or suppress the expression of Rho-A and ROCKⅡ. Our data suggested that the electroacupuncture could specifically inhibit the activation of the Rho/ROCK signaling pathway thus partially contributing to the repair of injured spinal cord. Monosialoganglioside could promote the motor function but did not suppress expression of Rho A and ROCKⅡ. There was no synergistic effect of electroacupuncture combined with monosialoganglioside.
文摘Propose:To investigate the molecular mechanisms underlying the protective effects of ischemic pre-conditioning(IPC)in patients undergoing total knee arthroplasty.Methods:GSE21164 was extracted from an online database,followed by an investigation of differentiallyexpressed genes(DEGs)between IPC treatment samples at 2 time points(T0T and T1T).Function andpathway enrichment analyses were performed on the DEGs.A protein-protein interaction network wasconstructed to identify hub genes according to 5 different algorithms,followed by enrichment analysis.In addition,long noncoding RNAs(lncRNAs)were identified between the T0T and T1T samples.Furthermore,a competing endogenous RNA network was predicted based on the identified lncRNA-messenger RNA(mRNA),lncRNA-microRNA(miRNA),and mRNA-miRNA relationships revealed in thisstudy.Finally,a drug-gene network was investigated.Statistical analyses were performed usingGraphPad Prism 8.0.Differences between groups were determined using an unpaired t-test.p<0.05 wasconsidered significant.Results:A total of 343 DEGs at T0 and 10 DEGs at T1 were identified and compared with their respectivecontrol groups,followed by 100 DEGs between T0T and T1T.Based on these 100 DEGs,protein-proteininteraction network analysis revealed 9 hub genes,mainly with mitochondria-related functions andthe carbon metabolism pathway.Six differentially expressed lncRNAs were investigated between T0T andT1T.A competing endogenous RNA network was constructed using 259 lncRNAemiRNAemRNA in-teractions,including alpha-2-macroglobulin antisense RNA 1-miR-7161-5p-iron-sulfur cluster scaffold.Finally,13 chemical drugs associated with the hub genes were explored.Conclusion:Iron-sulfur cluster scaffold may promote IPC-induced ischemic tolerance mediated by alpha-2-macroglobulin antisense RNA 1-miR-7161-5p axis.Moreover,IPC may induce a protective responseafter total knee arthroplasty via mitochondria-related functions and the carbon metabolism pathway,which should be further validated in the near future.
文摘Background Persistence of slow pathway (SP) function after SP modification is not uncommon after successful rediofrequency (RF) ablation of typical AV nodal reentry tachycardia (AVNRT). Methods and results We compared two methods (maximal AH interval during decremental atrial stimlation vs occurrence of AV nodal echos or dual AV nodal physiology (DAVNP): ≥50 msec increment in AH interval with a 10 msec decrement in A1A2) for the assessment of SP function immediately and 40 minutes after successful RF modification of SP. In 31 consecutive patients (age: 51±16 years, 18 women, 13 men) with typical AVNRT, SP modification was performed using a combined anatomic and electrogram guided approach. Immediately after successful SP modification, AV nodal function was assessed. This was repeated 40 minutes later. RF modification of SP was successful in all 31 patients. There was no recurrance during a 5±3 month follow up period. There was no significant difference between the electrophysiological parameters immediately and University of Frankfurt, Germany (Li YG, Bogun F, Grnefeld G, Hohnloser SH and Goethe JW)40 min after successful SP modification. There was evidence of SP function in 14 patients (6 with DAVNP+AV nodal echoes, 8 with either DAVNP or AV nodal echos) immehiately after SP modification. These patients could be differentiated from the patients without remaining SP function by maximal AH interval (298±102 msec vs 198±72 msec, P=0.004). 40 minutes after the suucessful SP modification, 11 patients displayed SP function (4 patients with DAVNP+AV nodal echos, 7 patients with either DAVNP or AV nodal echos). These patients could also be differentiated from the remaining patients with the use of the maximal AH interval (294±89 msec vs 189±50 msec, P<0.001).[BHDFG3,WK9ZQ,WK6,WK10*2,WK5W]Befroe SP modificationImmediately after RF40 min after RF[BHDZG1*2,WK9ZQ,WK6,WK10*2,WK5W]AVNERP (msec)258±44310±116316±114AVBCL (msec)330±55384±113376±110VABCL (msec)306±67306± 66311±54Max AH (msec)337±96247±100233±86 Conclusion SP function assessed immediately and 40 minutes after a successful SP modification remains stable. SP function can be assessed reliable by maximal AH interval during decremental atrial stimulation.
