A strain B34 against Thanatephorus cucumeris was screened from rice plants. Lab and field experiments showed that the control effects of this fungal strain were better than that of Jinggangmycin on PDA plate. Based on...A strain B34 against Thanatephorus cucumeris was screened from rice plants. Lab and field experiments showed that the control effects of this fungal strain were better than that of Jinggangmycin on PDA plate. Based on the chemical components of cell wall and physiological and biochemical characters of B34, the fungal was named as Pseudomonas aureofaciens. It was a new antagonistic strain against Thanatephorus cucumeris.展开更多
Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
Chronic stress can induce hippocampus injury such as neuron loss and dendrite atrophy,but its mechanism and molecular basis remain unclear up to now.To understand the molecular mechanism on protein level and find the ...Chronic stress can induce hippocampus injury such as neuron loss and dendrite atrophy,but its mechanism and molecular basis remain unclear up to now.To understand the molecular mechanism on protein level and find the crucial proteins which correlated with chronic展开更多
Vascular tissue serves as the channel for nutrient transport and signal transduc-tion between different organs in plants. To study molecular identity and behavior of mobile substances transmitted between organs via ...Vascular tissue serves as the channel for nutrient transport and signal transduc-tion between different organs in plants. To study molecular identity and behavior of mobile substances transmitted between organs via vascular tissue, it is necessary to collect exudate from stem or other organs. Modifed stem-cutting method for exudate collection in soybean was used in this study by selecting the optimum sampling time and position, using reagents preventing RNA degradation, etc. Diurnal dynamics analysis of exudate emission was found to be the highest during 10：00-10：10 am. Totally 15 μL pure exudate was collected from the stem cut between cotyledonary and unifoliolate nodes at V1 stage （unifoliolate just expanded） of young soybean seedling. Improved TRIzol method was used to extract RNA and protein from stem exudate. A phloem specifc gene of Glycine max sieve element occlusion s, SEO, in exudate samples was successfully amplifed by RT-PCR, which comfrmed the success of RNA extraction. SDS-PAGE showed the majority of proteins in exudate were of low molec-ular weight. Method proposed in this study would facilitate collection of quality exudate and enhance further investigation of mobile substances in soybean.展开更多
OBJECTIVE:This study screened serum tumor biomarkers by surface enhanced laser desorption/ionization time-of-flight mass spectrometry(SELDI-TOF-MS) to establish a subset which could be used for the prediction of Qi de...OBJECTIVE:This study screened serum tumor biomarkers by surface enhanced laser desorption/ionization time-of-flight mass spectrometry(SELDI-TOF-MS) to establish a subset which could be used for the prediction of Qi deficiency syndrome and phlegm and blood stasis in patients with non-small cell lung cancer;and as diagnostic model of Chinese medicine.METHODS:Serum samples from 63 lung cancer patients with Qi deficiency syndrome and phlegm and blood stasis,and 28 lung cancer patients with non-Qi deficiency syndrome and phlegm and blood stasis were analyzed using SELDI-TOF-MS with a PBS II-C protein chip reader.Protein profiles were generated using immobilized metal affinity capture(IMAC3) protein chips.Differentially-expressed proteins were screened.Protein peak clustering and classification analyses were performed using Biomarker Wizard and Biomarker Pattern software packages,respectively.RESULTS:A total of 268 effective protein peaks were detected in the 1,000-10,000 Da molecular range for the 15 serum proteins screened(P<0.05).The decision tree model was M 2284.97,with a sensitivity of 96.2% and a specificity of 66.7%.CONCLUSION:SELDI-TOF-MS techniques,combined with a decision tree model,can help identify serum proteomic biomarkers related to Qi deficiency syndrome and phlegm and blood stasis in lung cancer patients;and the predictive model can be used to discriminate between Chinese medicine diagnostic models of disease.展开更多
An assay was described for measures of adducts of styrene oxide (SO) with molecules of hemoglobin(Hb) which have been modified at residues containing either carboxylic acid or sulfhydryl groups. The method employs tw...An assay was described for measures of adducts of styrene oxide (SO) with molecules of hemoglobin(Hb) which have been modified at residues containing either carboxylic acid or sulfhydryl groups. The method employs two steps. In the first, SO carboxylic acid adducts are hydrolyzed in basic medium to liberate styrene glycol(SG). Then, the remaining residues are reacted with a reductive catalyst (Raney nickel) to liberate the two positional isomers of SO cysteine adducts, i.e., 1 phenylethanol (1 PE) and 2 phenylethanol (2 PE). The liberated products are derivatized with pentafluorobenzoyl chloride and measured by GC NICI MS. The assay was evaluated with SO adducts of Hb which had been produced in the blood of Sprague Dawley rats following (a) in vitro modification(0—300m mol/L SO) or (b) i.p administration of either SO(0—1 mmol/kg) or styrene (0—3 mmol/kg). Levels of each of the three analytes (SG, 1 PE, and 2 PE) increased with dose in hemoglobin. The ratios of cysteine adducts to carboxylic acid adducts varied significantly among experiments. Ratios of 2 PE to 1 PE were much more consistent (2 PE/1 PE=6.9 (SE=1.5)) suggesting that binding of SO to cysteine residues of blood proteins is greatly preferred at the α position rather than the β position both in vitro and in vivo. The lowest detectable adduct concentration, using 10 mg of protein, was 8 pmol/g protein for SG,5 pmol/g protein for 1 PE, and 0.6 pmol/g protein for 2 PE. No significant change of adduct level was found during storage of proteins at -80℃ for 1 year.展开更多
This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an import...This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.展开更多
Homogenates prepared from S. japonicum adult worms ofdifferent isolates from Anhui, Hubei, Guangxi, Yunnan andSichuan Provinces were analyzed by SDS-PAGE and enzymelinked immunoelectrotransfer blot (EITB) tested with ...Homogenates prepared from S. japonicum adult worms ofdifferent isolates from Anhui, Hubei, Guangxi, Yunnan andSichuan Provinces were analyzed by SDS-PAGE and enzymelinked immunoelectrotransfer blot (EITB) tested with rabbitanti-snails antibody. The results of SDS-PAGE indicated thatwith silver staining both male and female worms of Guangxiisolate showed some definite differences in their protein profile,namely, absence of one band between 50-75 kDa in maleworms and marked reduction in quantity of > 110 and 30 kDabands in female worms. There was no obvious differenceamong other isolates both in male and female worms. TheEITB patterns were similar in S. japonicum of Anhui andHubei, and it was also the case with isolates from Yunnan andSichuau, except that Yuunan female worms had a distinct band展开更多
Foot-and-mouth disease virus(FMDV) is the causative agent of a highly contagious disease in livestock. The viral proteinaseL^(rop) of FMDV is involved in pathogenicity, and mutation of theL^(rop) SAP domain reduces FM...Foot-and-mouth disease virus(FMDV) is the causative agent of a highly contagious disease in livestock. The viral proteinaseL^(rop) of FMDV is involved in pathogenicity, and mutation of theL^(rop) SAP domain reduces FMDV pathogenicity in pigs. To determine the gene expression profiles associated with decreased pathogenicity in porcine cells, we performed transcriptome analysis using next-generation sequencing technology and compared differentially expressed genes in SK6 cells infected with FMDV containingL^(rop) with either a wild-type or mutated version of the SAP domain. This analysis yielded 1,853 genes that exhibited a ≥ 2-fold change in expression and was validated by real-time quantitative PCR detection of several differentially expressed genes. Many of the differentially expressed genes correlated with antiviral responses corresponded to genes associated with transcription factors, immune regulation, cytokine production, inflammatory response, and apoptosis. Alterations in gene expression profiles may be responsible for the variations in pathogenicity observed between the two FMDV variants. Our results provided genes of interest for the further study of antiviral pathways and pathogenic mechanisms related to FMDV L^(rop).展开更多
The nucleotide sequence deduced from the amino acid sequence of the scorpion insectotoxin AaIT was chemically synthesized and was expressed in Escherichia coli. The authenticity of this in vitro expressed peptide was ...The nucleotide sequence deduced from the amino acid sequence of the scorpion insectotoxin AaIT was chemically synthesized and was expressed in Escherichia coli. The authenticity of this in vitro expressed peptide was confirmed by N-terminal peptide sequencing. Two groups of bioassays, artificial diet incorporation assay and contact insecticidal effect assay, were carried out separately to verify the toxicity of this recombinant toxin. At the end of a 24 h experimental period, more than 60% of the testing diamondback moth (Plutella xylostella) larvae were killed in both groups with LC50 value of 18.4 microM and 0.70 microM respectively. Cytotoxicity assay using cultured Sf9 insect cells and MCF-7 human cells demonstrated that the toxin AaIT had specific toxicity against insect cells but not human cells. Only 0.13 microM recombinant toxin was needed to kill 50% of cultured insect cells while as much as 1.3 microM toxin had absolutely no effect on human cells. Insect cells produced obvious intrusions from their plasma membrane before broken up. We infer that toxin AaIT bind to a putative sodium channel in these insect cells and open the channel persistently, which would result in Na+ influx and finally cause destruction of insect cells.展开更多
MCM10 protein is an essential replication factor involved in the initiation of DNA replication. A mcm10 mutant (mcm10-1) of budding yeast shows a growth arrest at 37 degrees C. In the present work, we have isolated a ...MCM10 protein is an essential replication factor involved in the initiation of DNA replication. A mcm10 mutant (mcm10-1) of budding yeast shows a growth arrest at 37 degrees C. In the present work, we have isolated a mcm10-1 suppressor strain, which grows at 37 degrees C. Interestingly, this mcm10-1 suppressor undergoes cell cycle arrest at 14 degrees C. A novel gene, YLR003c, is identified by high-copy complementation of this suppressor. We called it as Cms1 (Complementation of Mcm 10 Suppressor). Furthermore, the experiments of transformation show that cells of mcm10-1 suppressor with high-copy plasmid but not low-copy plasmid grow at 14 degrees C, indicating that overexpression of Cms1 can rescue the growth arrest of this mcm10 suppressor at non-permissive temperature. These results suggest that CMS1 protein may functionally interact with MCM10 protein and play a role in the regulation of DNA replication and cell cycle control.展开更多
Background Von HippeI-Lindau disease （VHL）,a heritable autosomal dominant disease characterized by neoplasia in multiple organ systems,has rarely been reported in Asia.We genetically investigated a unique Chinese fa...Background Von HippeI-Lindau disease （VHL）,a heritable autosomal dominant disease characterized by neoplasia in multiple organ systems,has rarely been reported in Asia.We genetically investigated a unique Chinese family with VHL disease and performed an analysis of the VHL protein stability.Methods Genomic deoxyribonucleic acid （DNA） extracted from peripheral blood was amplified by polymerase chain reaction （PCR） to three exons of the VHL gene in 9 members of the Chinese family with VHL disease.PCR products were directly sequenced.We estimated the effects of VHL gene mutation on the stability of pVHL,which is indicated by the free energy difference between the wild-type and the mutant protein （△△G）.Results The Chinese family was classified as VHL type 1.Three family members,including two patients and a carrier,had a T to G heterozygotic missense mutation at nucleotide 515 of the VHL gene exon 1.This missense mutation resulted in the transition from leucine to arginine in amino acid 101 of the VHL protein.There was low stability of the VHL protein （the △△G was 12.71 kcal/mol） caused by this missense mutation.Conclusions We first reported a family with this VHL gene mutation in Asia.This missense mutation is predicted to significantly reduce the stability of the VHL protein and contribute to the development of the renal cell carcinoma （RCC） phenotype displayed by this family.The genetic characterization and protein stability analysis of families with VHL disease are important for early diagnosis and prevention of the disease being passed on to their offspring.展开更多
Machine intelligence,is out of the system by the artificial intelligence shown.It is usually achieved by the average computer intelligence.Rough sets and Information Granules in uncertainty management and soft computi...Machine intelligence,is out of the system by the artificial intelligence shown.It is usually achieved by the average computer intelligence.Rough sets and Information Granules in uncertainty management and soft computing and granular computing is widely used in many fields,such as in protein sequence analysis and biobasis determination,TSM and Web service classification Etc.展开更多
Protein analysis is vital for biological and clinical research, but the measurement of unseparated, intact and high-mass proteins is also a challenging task by mass spectrometry-based methods. Here, we present a proto...Protein analysis is vital for biological and clinical research, but the measurement of unseparated, intact and high-mass proteins is also a challenging task by mass spectrometry-based methods. Here, we present a protocol for rapid and high-throughput analysis of intact proteins in tissue samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry（MALDITOF MS） combined with a high-mass detector platform. The method involves tissue specimens that undergo a simple protein extraction before MALDI-MS analysis. Using this method, the high abundance proteins in human thyroid carcinoma and paracarcinoma tissues were successfully investigated, and the mass spectra of the tissues of the 30 illustrated thyroid cancers showed remarkable differences. The peak intensity revealed a significant increase in human albumin in thyroid carcinoma tissues（p＆lt;0.05）. To validate the feasibility and credibility of this method, label-free proteomics quantitative analysis and Western blotting were used to relatively quantify the proteins in these tissues. Those results demonstrated a nearly 3-fold difference in human albumin levels between thyroid carcinoma and para-carcinoma tissues, which were consistent with the results of our method. The advantages of our method are easy sample handling, remarkable reproducibility and the ability to analyze high-mass proteins without digestion, which make them have the potential to be used in biological research and in clinical practice.展开更多
Mitotic catastrophe(MC)is a form of programmed cell death induced by mitotic process disorders,which is very important in tumor prevention,development,and drug resistance.Because rapidly increased data for MC is vigor...Mitotic catastrophe(MC)is a form of programmed cell death induced by mitotic process disorders,which is very important in tumor prevention,development,and drug resistance.Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study,it is urgent for us to develop a professional and comprehensive database to curate MC-related data.Mitotic Catastrophe Database(MCDB)consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles.Also,MCDB defines the confidence level,classification criteria,and uniform naming rules for MC-related data,which greatly improves data reliability and retrieval convenience.Moreover,MCDB develops protein sequence alignment and target prediction functions.The former can be used to predict new potential MC-related genes and proteins,and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds.In short,MCDB is such a proprietary,standard,and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry,molecular biology,bioinformatics,oncology and so on.The MCDB is distributed on http://www.combio-lezhang.online/MCDB/indexhtml/.展开更多
Objective： To investigate the effects of acupuncture on the number of associated phosphorylated proteins in brain tissues of middle cerebral artery occlusion （MCAO） rats, based on the protein microarray technique. ...Objective： To investigate the effects of acupuncture on the number of associated phosphorylated proteins in brain tissues of middle cerebral artery occlusion （MCAO） rats, based on the protein microarray technique. Methods： The MCAO model was prepared according to the modified occlusion method using occlusion lines. Forty healthy Sprague-Dawley （SD） rats were randomly divided into 4 groups using the lottery method： a sham operation group, a model group, a control point group and an acupoint group, with 10 rats in each group. Rats in the sham operation group and the model group only received binding without acupuncture. Rats in the acupoint group received acupuncture at Dazhui （GV 14）, Baihui （GV 20） and Shuigou （GV 25）; rats in the control point group received acupuncture at non-acupoint control points. The needle was twisted once for 1 min after insertion and another time in the middle of the 30 min needle retaining. Acupuncture was conducted once every 12 h for 6 consecutive times. At the end of the experiment, the neurological impairment score was collected, and cells of the ischemic brain tissues were extracted. The protein phosphorylation of the related signaling was detected using the 720 phosphorylated antibody microarray technique, and the differentially expressed proteins between groups were screened. Results： The neurological impairment scores after 72 h of treatment： compared with the sham operation group, the scores of the model group, the control point group and the acupoint group were significantly increased （P〈0.01）; compared with the model group, the scores of the acupoint group and the control point group were significantly decreased （P〈0.01,P〈0.05）; the score of the acupoint group was better than that of the control point group （P〈0.05）. The results of the protein microarray： compared with the sham operation group, 48 proteins showed up-regulated phosphorylation （≥1.5 times） in the model group and the down-regulated was 28; compared with the model group, 35 proteins showed up-regulated phosphorylation in the control point group, and the down-regulated was 24. There were 29 proteins showing up-regulated phosphorylation in the acupoint group and the down-regulated was 51. The numbers of proteins involved in the function and signal transduction pathways were also different. Conclusion： Acupuncture at Dazhui （GV 14）, Baihui （GV 20） and Shuigou （GV 25） can effectively repair brain injury. The ischemic injury of brain tissue may be caused by imbalance of a variety of proteins, and acupuncture can promote brain tissue repair by multi-functional and multi-channel regulation of the protein disorders.展开更多
Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase （SAHH） and adenosine kinase （ADK） act coordinately to recycle the by-product of these reac...Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase （SAHH） and adenosine kinase （ADK） act coordinately to recycle the by-product of these reactions, S-adenosylhomocysteine （SAH） that would otherwise competitively inhibit methyltransferase （MT） activities. Here, we report on investigations to understand how the SAH produced in the nucleus is metabolized by SAHH and ADK. Localization analyses using green fluorescent fusion proteins demonstrated that both enzymes are capable of localizing to the cytoplasm and the nucleus, although no obvious nuclear localization signal was found in their sequences. Deletion analysis revealed that a 41-amino-acid segment of SAHH （GlylS^-Lys19~） is required for nuclear targeting of this enzyme. This segment is surface exposed, shows unique sequence conservation patterns in plant SAHHs, and possesses additional features of protein-protein interaction motifs. ADK and SAHH interact in Arabidopsb via this segment and also interact with an mRNA cap MT. We propose that the targeting of this complex is directed by the nuclear localization signal of the MT; other MTs may similarly target SAHH/ADK to other subcellular compartments to ensure uninterrupted transmethylation.展开更多
Digital microfluidics technology offers a platform for developing diagnostic applications with the advantages of portability,sample and reagent volume reduction,faster analysis,increased automation,low power consumpti...Digital microfluidics technology offers a platform for developing diagnostic applications with the advantages of portability,sample and reagent volume reduction,faster analysis,increased automation,low power consumption,compatibility with mass manufacturing and high throughput.In addition to diagnostics,digital microfluidics is finding use in nucleic acid analysis,peptide and protein analysis,cell analysis,drug analysis and delivery and immunization analysis.In this review,we describe these applications,their implementation,and associated design issues.As other review in the digital microfluidics technology,there have been and will be unexpected developments as DMF matures,but we predict that the future is bright for this promising technology at the last section.展开更多
Background The non-hemodynamic effects of angiotensin receptor blocker （ARB） in the delay of progression of chronic kidney disease （CKD） remain unclear. In this study, we investigated the influence of irbesartan o...Background The non-hemodynamic effects of angiotensin receptor blocker （ARB） in the delay of progression of chronic kidney disease （CKD） remain unclear. In this study, we investigated the influence of irbesartan on the urinary excretion of cytokines in patients with CKD. Methods In this randomized perspective clinical trial, different doses of irbesartan （150 mg/d and 300 mg/d） were given to two groups of patients in a cross-over design. Blood pressure （BP）, creatinine clearance （Ccr） and 24-hour proteinuria were examined. Urinary excretion of cytokines was determined by human inflammatory cytokine antibody array. A two-fold change in spot intensity was considered significant. Results Urinary excretion of cytokines （granulocyte colony stimulating factor （GCSF）, intercellular cell adhesion molecule-1 （ICAM-1）, interferon y （IFN-y）, interleukin 1β （IL-1β）, IL-2, IL-6, IL-8, IL-11, IL-15 and macrophage inflammatory protein 1δ （MIP-Iδ） in group B （irbesartan 300 mg/d） was significantly decreased in comparison to group A （irbesartan 150 mg/d） after 8-week treatment. In group A, 8 weeks of treatment induced a two- to nine-fold reduction in urinary cytokine levels （GCSF, GM-CSF, IFN-γ, IL-1α, IL-11, IL-12p40, MCP-2, MIP-1α）, while increasing the dosage to 300 mg/d further decreased the excretion of GCSF, GM-CSF, IL-12p40, MCP-2 and MIP-1α by week 18. There was no significant difference in BP or Ccr between the two groups. However, 24-hour proteinuria was significantly reduced in both groups, and in group A the reduction was dose dependent.Conclusion Irbesartan offers additional renoprotection in a dose-dependent manner by reducing pro-inflammatory cvtokines excretion in the urine of CKD patients.展开更多
Background Neuroblastoma （NB） is one of the most common malignant solid tumors of childhood.It is still not clear whether the apoptosis of tumor cells or the non-tumor cells contributes to the increase of concentrat...Background Neuroblastoma （NB） is one of the most common malignant solid tumors of childhood.It is still not clear whether the apoptosis of tumor cells or the non-tumor cells contributes to the increase of concentration of cytochrome c （Cyt c） in the serum of the cancer patients.The aim of this research was to identify the source of the Cyt c in the serum when the tumor grows up by subcutaneous inoculation of human NB cells into nude mice.Methods We subcutaneously inoculated human NB cells （KP-N-NS） into nude mice and collected the sera of tumor-bearing mice （n=14） and control mice （n=25） 4 weeks later in order to screen for and identify differentially expressed proteins in the serum.Differentially expressed proteins in the serum were screened by surface-enhanced laser desorption/ionization-time-of-fiight （SELDI-TOF） mass spectrometry.Results The relative intensity of a protein having a mass-to-charge ratio （m/z） of 11 609 was 3338.37±3410.85 in the tumor group and 59.84±40.74 in the control group,indicating that the expression level of this protein in the tumor group was 55.8 times higher than that in the control group.Serum proteins were separated and purified by high-performance liquid chromatography （HPLC）.Liquid chromatography coupled with tandem mass spectrometry （LC-MS/MS） was performed to produce peptide mass fingerprints （PMFs）.Spectrum analysis and a database search revealed that the highly expressed protein （m/z=11605.4） from the serum of tumor-bearing mice was the mouse Cyt c.Conclusions Increased concentration of Cyt c in the serum of tumor-bearing nude mice might be partially attributed to the secretion of this protein by non-tumor cells.展开更多
文摘A strain B34 against Thanatephorus cucumeris was screened from rice plants. Lab and field experiments showed that the control effects of this fungal strain were better than that of Jinggangmycin on PDA plate. Based on the chemical components of cell wall and physiological and biochemical characters of B34, the fungal was named as Pseudomonas aureofaciens. It was a new antagonistic strain against Thanatephorus cucumeris.
文摘Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
文摘Chronic stress can induce hippocampus injury such as neuron loss and dendrite atrophy,but its mechanism and molecular basis remain unclear up to now.To understand the molecular mechanism on protein level and find the crucial proteins which correlated with chronic
基金funded by China Agriculture Research system(CARS-04)CAAS Agricultural Sciences and Technology Innovation Project
文摘Vascular tissue serves as the channel for nutrient transport and signal transduc-tion between different organs in plants. To study molecular identity and behavior of mobile substances transmitted between organs via vascular tissue, it is necessary to collect exudate from stem or other organs. Modifed stem-cutting method for exudate collection in soybean was used in this study by selecting the optimum sampling time and position, using reagents preventing RNA degradation, etc. Diurnal dynamics analysis of exudate emission was found to be the highest during 10：00-10：10 am. Totally 15 μL pure exudate was collected from the stem cut between cotyledonary and unifoliolate nodes at V1 stage （unifoliolate just expanded） of young soybean seedling. Improved TRIzol method was used to extract RNA and protein from stem exudate. A phloem specifc gene of Glycine max sieve element occlusion s, SEO, in exudate samples was successfully amplifed by RT-PCR, which comfrmed the success of RNA extraction. SDS-PAGE showed the majority of proteins in exudate were of low molec-ular weight. Method proposed in this study would facilitate collection of quality exudate and enhance further investigation of mobile substances in soybean.
基金Supported by the National Natural Science Foundation of China(No.30572293)the "Eleventh Five" TCM Foundation for Major Clinical Research of PLA(No.2006051002)the Natural Science Foundation of Fujian Province,China(No. 2010J01197)
文摘OBJECTIVE:This study screened serum tumor biomarkers by surface enhanced laser desorption/ionization time-of-flight mass spectrometry(SELDI-TOF-MS) to establish a subset which could be used for the prediction of Qi deficiency syndrome and phlegm and blood stasis in patients with non-small cell lung cancer;and as diagnostic model of Chinese medicine.METHODS:Serum samples from 63 lung cancer patients with Qi deficiency syndrome and phlegm and blood stasis,and 28 lung cancer patients with non-Qi deficiency syndrome and phlegm and blood stasis were analyzed using SELDI-TOF-MS with a PBS II-C protein chip reader.Protein profiles were generated using immobilized metal affinity capture(IMAC3) protein chips.Differentially-expressed proteins were screened.Protein peak clustering and classification analyses were performed using Biomarker Wizard and Biomarker Pattern software packages,respectively.RESULTS:A total of 268 effective protein peaks were detected in the 1,000-10,000 Da molecular range for the 15 serum proteins screened(P<0.05).The decision tree model was M 2284.97,with a sensitivity of 96.2% and a specificity of 66.7%.CONCLUSION:SELDI-TOF-MS techniques,combined with a decision tree model,can help identify serum proteomic biomarkers related to Qi deficiency syndrome and phlegm and blood stasis in lung cancer patients;and the predictive model can be used to discriminate between Chinese medicine diagnostic models of disease.
文摘An assay was described for measures of adducts of styrene oxide (SO) with molecules of hemoglobin(Hb) which have been modified at residues containing either carboxylic acid or sulfhydryl groups. The method employs two steps. In the first, SO carboxylic acid adducts are hydrolyzed in basic medium to liberate styrene glycol(SG). Then, the remaining residues are reacted with a reductive catalyst (Raney nickel) to liberate the two positional isomers of SO cysteine adducts, i.e., 1 phenylethanol (1 PE) and 2 phenylethanol (2 PE). The liberated products are derivatized with pentafluorobenzoyl chloride and measured by GC NICI MS. The assay was evaluated with SO adducts of Hb which had been produced in the blood of Sprague Dawley rats following (a) in vitro modification(0—300m mol/L SO) or (b) i.p administration of either SO(0—1 mmol/kg) or styrene (0—3 mmol/kg). Levels of each of the three analytes (SG, 1 PE, and 2 PE) increased with dose in hemoglobin. The ratios of cysteine adducts to carboxylic acid adducts varied significantly among experiments. Ratios of 2 PE to 1 PE were much more consistent (2 PE/1 PE=6.9 (SE=1.5)) suggesting that binding of SO to cysteine residues of blood proteins is greatly preferred at the α position rather than the β position both in vitro and in vivo. The lowest detectable adduct concentration, using 10 mg of protein, was 8 pmol/g protein for SG,5 pmol/g protein for 1 PE, and 0.6 pmol/g protein for 2 PE. No significant change of adduct level was found during storage of proteins at -80℃ for 1 year.
文摘This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.
基金This project was supported by the National Natural Science Foundation of China
文摘Homogenates prepared from S. japonicum adult worms ofdifferent isolates from Anhui, Hubei, Guangxi, Yunnan andSichuan Provinces were analyzed by SDS-PAGE and enzymelinked immunoelectrotransfer blot (EITB) tested with rabbitanti-snails antibody. The results of SDS-PAGE indicated thatwith silver staining both male and female worms of Guangxiisolate showed some definite differences in their protein profile,namely, absence of one band between 50-75 kDa in maleworms and marked reduction in quantity of > 110 and 30 kDabands in female worms. There was no obvious differenceamong other isolates both in male and female worms. TheEITB patterns were similar in S. japonicum of Anhui andHubei, and it was also the case with isolates from Yunnan andSichuau, except that Yuunan female worms had a distinct band
基金supported by grants from the National Science and Technology Ministry (2015BAD12B04)National Natural Sciences Foundation of China (No.31302118,31502042 and 31402179)+2 种基金the Gansu Science Foundation for Distinguished Young Scholars (no.145RJDA328)the International Atomic Energy Agency (16025/R0)the Key technologies R&Dprogram of Gansu Province (1302NKDA027)
文摘Foot-and-mouth disease virus(FMDV) is the causative agent of a highly contagious disease in livestock. The viral proteinaseL^(rop) of FMDV is involved in pathogenicity, and mutation of theL^(rop) SAP domain reduces FMDV pathogenicity in pigs. To determine the gene expression profiles associated with decreased pathogenicity in porcine cells, we performed transcriptome analysis using next-generation sequencing technology and compared differentially expressed genes in SK6 cells infected with FMDV containingL^(rop) with either a wild-type or mutated version of the SAP domain. This analysis yielded 1,853 genes that exhibited a ≥ 2-fold change in expression and was validated by real-time quantitative PCR detection of several differentially expressed genes. Many of the differentially expressed genes correlated with antiviral responses corresponded to genes associated with transcription factors, immune regulation, cytokine production, inflammatory response, and apoptosis. Alterations in gene expression profiles may be responsible for the variations in pathogenicity observed between the two FMDV variants. Our results provided genes of interest for the further study of antiviral pathways and pathogenic mechanisms related to FMDV L^(rop).
基金This work was supported by a grant from 863High Technology Program,Chinese Ministry of Sci-ence and Technology
文摘The nucleotide sequence deduced from the amino acid sequence of the scorpion insectotoxin AaIT was chemically synthesized and was expressed in Escherichia coli. The authenticity of this in vitro expressed peptide was confirmed by N-terminal peptide sequencing. Two groups of bioassays, artificial diet incorporation assay and contact insecticidal effect assay, were carried out separately to verify the toxicity of this recombinant toxin. At the end of a 24 h experimental period, more than 60% of the testing diamondback moth (Plutella xylostella) larvae were killed in both groups with LC50 value of 18.4 microM and 0.70 microM respectively. Cytotoxicity assay using cultured Sf9 insect cells and MCF-7 human cells demonstrated that the toxin AaIT had specific toxicity against insect cells but not human cells. Only 0.13 microM recombinant toxin was needed to kill 50% of cultured insect cells while as much as 1.3 microM toxin had absolutely no effect on human cells. Insect cells produced obvious intrusions from their plasma membrane before broken up. We infer that toxin AaIT bind to a putative sodium channel in these insect cells and open the channel persistently, which would result in Na+ influx and finally cause destruction of insect cells.
文摘MCM10 protein is an essential replication factor involved in the initiation of DNA replication. A mcm10 mutant (mcm10-1) of budding yeast shows a growth arrest at 37 degrees C. In the present work, we have isolated a mcm10-1 suppressor strain, which grows at 37 degrees C. Interestingly, this mcm10-1 suppressor undergoes cell cycle arrest at 14 degrees C. A novel gene, YLR003c, is identified by high-copy complementation of this suppressor. We called it as Cms1 (Complementation of Mcm 10 Suppressor). Furthermore, the experiments of transformation show that cells of mcm10-1 suppressor with high-copy plasmid but not low-copy plasmid grow at 14 degrees C, indicating that overexpression of Cms1 can rescue the growth arrest of this mcm10 suppressor at non-permissive temperature. These results suggest that CMS1 protein may functionally interact with MCM10 protein and play a role in the regulation of DNA replication and cell cycle control.
基金This research was supported by grants from the National Natural Science Foundation of China （No. 30901487, No. 81302223, No. 81070488 and No. 81172432）, the Guangdong Natural Science Foundation （No. 10251008901000005）, and the Guangdong Province Science and Technology Project （No. 2011 B031800115, No. 2011 B032000003 and No. 20101051500032）.
文摘Background Von HippeI-Lindau disease （VHL）,a heritable autosomal dominant disease characterized by neoplasia in multiple organ systems,has rarely been reported in Asia.We genetically investigated a unique Chinese family with VHL disease and performed an analysis of the VHL protein stability.Methods Genomic deoxyribonucleic acid （DNA） extracted from peripheral blood was amplified by polymerase chain reaction （PCR） to three exons of the VHL gene in 9 members of the Chinese family with VHL disease.PCR products were directly sequenced.We estimated the effects of VHL gene mutation on the stability of pVHL,which is indicated by the free energy difference between the wild-type and the mutant protein （△△G）.Results The Chinese family was classified as VHL type 1.Three family members,including two patients and a carrier,had a T to G heterozygotic missense mutation at nucleotide 515 of the VHL gene exon 1.This missense mutation resulted in the transition from leucine to arginine in amino acid 101 of the VHL protein.There was low stability of the VHL protein （the △△G was 12.71 kcal/mol） caused by this missense mutation.Conclusions We first reported a family with this VHL gene mutation in Asia.This missense mutation is predicted to significantly reduce the stability of the VHL protein and contribute to the development of the renal cell carcinoma （RCC） phenotype displayed by this family.The genetic characterization and protein stability analysis of families with VHL disease are important for early diagnosis and prevention of the disease being passed on to their offspring.
文摘Machine intelligence,is out of the system by the artificial intelligence shown.It is usually achieved by the average computer intelligence.Rough sets and Information Granules in uncertainty management and soft computing and granular computing is widely used in many fields,such as in protein sequence analysis and biobasis determination,TSM and Web service classification Etc.
基金supported by the National Natural Science Foundation of China (21672250)Chinese Academy of Sciences (YZ201544)+1 种基金National Key Technology Support Program (2015BAK45B01)the Shanghai Municipal Planning Commission of Science and Research Fund for Young Scholar (20154Y0050)
文摘Protein analysis is vital for biological and clinical research, but the measurement of unseparated, intact and high-mass proteins is also a challenging task by mass spectrometry-based methods. Here, we present a protocol for rapid and high-throughput analysis of intact proteins in tissue samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry（MALDITOF MS） combined with a high-mass detector platform. The method involves tissue specimens that undergo a simple protein extraction before MALDI-MS analysis. Using this method, the high abundance proteins in human thyroid carcinoma and paracarcinoma tissues were successfully investigated, and the mass spectra of the tissues of the 30 illustrated thyroid cancers showed remarkable differences. The peak intensity revealed a significant increase in human albumin in thyroid carcinoma tissues（p＆lt;0.05）. To validate the feasibility and credibility of this method, label-free proteomics quantitative analysis and Western blotting were used to relatively quantify the proteins in these tissues. Those results demonstrated a nearly 3-fold difference in human albumin levels between thyroid carcinoma and para-carcinoma tissues, which were consistent with the results of our method. The advantages of our method are easy sample handling, remarkable reproducibility and the ability to analyze high-mass proteins without digestion, which make them have the potential to be used in biological research and in clinical practice.
基金supported by grants from National Natural Science Foundation of China(Grant Nos.81803755 and 81922064)National Science and Technology Major Project(Grant No.2018ZX10201002,China)+1 种基金China Postdoctoral ScienceFoundation(2018M640926 and 2020M673221)Sichuan University Postdoctoral Research and Development Foundation(2020SCU12062 and 2020SCU12056,China)。
文摘Mitotic catastrophe(MC)is a form of programmed cell death induced by mitotic process disorders,which is very important in tumor prevention,development,and drug resistance.Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study,it is urgent for us to develop a professional and comprehensive database to curate MC-related data.Mitotic Catastrophe Database(MCDB)consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles.Also,MCDB defines the confidence level,classification criteria,and uniform naming rules for MC-related data,which greatly improves data reliability and retrieval convenience.Moreover,MCDB develops protein sequence alignment and target prediction functions.The former can be used to predict new potential MC-related genes and proteins,and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds.In short,MCDB is such a proprietary,standard,and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry,molecular biology,bioinformatics,oncology and so on.The MCDB is distributed on http://www.combio-lezhang.online/MCDB/indexhtml/.
基金supported by National Natural Science Foundation of China No. 81303051, No. 30901901Province and Ministry Co-construction Key Laboratory for Internal Medicine of Traditional Chinese Medicine of the Education Ministry of China No. ZYNK201501+1 种基金Tuina Department of Yueyang Hostpital Affiliated to Hunan University of Chinese Medicine State Clinical Key SpecialtyTuina Key Discipline of State Administration of Traditional Chinese Medicine~~
文摘Objective： To investigate the effects of acupuncture on the number of associated phosphorylated proteins in brain tissues of middle cerebral artery occlusion （MCAO） rats, based on the protein microarray technique. Methods： The MCAO model was prepared according to the modified occlusion method using occlusion lines. Forty healthy Sprague-Dawley （SD） rats were randomly divided into 4 groups using the lottery method： a sham operation group, a model group, a control point group and an acupoint group, with 10 rats in each group. Rats in the sham operation group and the model group only received binding without acupuncture. Rats in the acupoint group received acupuncture at Dazhui （GV 14）, Baihui （GV 20） and Shuigou （GV 25）; rats in the control point group received acupuncture at non-acupoint control points. The needle was twisted once for 1 min after insertion and another time in the middle of the 30 min needle retaining. Acupuncture was conducted once every 12 h for 6 consecutive times. At the end of the experiment, the neurological impairment score was collected, and cells of the ischemic brain tissues were extracted. The protein phosphorylation of the related signaling was detected using the 720 phosphorylated antibody microarray technique, and the differentially expressed proteins between groups were screened. Results： The neurological impairment scores after 72 h of treatment： compared with the sham operation group, the scores of the model group, the control point group and the acupoint group were significantly increased （P〈0.01）; compared with the model group, the scores of the acupoint group and the control point group were significantly decreased （P〈0.01,P〈0.05）; the score of the acupoint group was better than that of the control point group （P〈0.05）. The results of the protein microarray： compared with the sham operation group, 48 proteins showed up-regulated phosphorylation （≥1.5 times） in the model group and the down-regulated was 28; compared with the model group, 35 proteins showed up-regulated phosphorylation in the control point group, and the down-regulated was 24. There were 29 proteins showing up-regulated phosphorylation in the acupoint group and the down-regulated was 51. The numbers of proteins involved in the function and signal transduction pathways were also different. Conclusion： Acupuncture at Dazhui （GV 14）, Baihui （GV 20） and Shuigou （GV 25） can effectively repair brain injury. The ischemic injury of brain tissue may be caused by imbalance of a variety of proteins, and acupuncture can promote brain tissue repair by multi-functional and multi-channel regulation of the protein disorders.
文摘Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase （SAHH） and adenosine kinase （ADK） act coordinately to recycle the by-product of these reactions, S-adenosylhomocysteine （SAH） that would otherwise competitively inhibit methyltransferase （MT） activities. Here, we report on investigations to understand how the SAH produced in the nucleus is metabolized by SAHH and ADK. Localization analyses using green fluorescent fusion proteins demonstrated that both enzymes are capable of localizing to the cytoplasm and the nucleus, although no obvious nuclear localization signal was found in their sequences. Deletion analysis revealed that a 41-amino-acid segment of SAHH （GlylS^-Lys19~） is required for nuclear targeting of this enzyme. This segment is surface exposed, shows unique sequence conservation patterns in plant SAHHs, and possesses additional features of protein-protein interaction motifs. ADK and SAHH interact in Arabidopsb via this segment and also interact with an mRNA cap MT. We propose that the targeting of this complex is directed by the nuclear localization signal of the MT; other MTs may similarly target SAHH/ADK to other subcellular compartments to ensure uninterrupted transmethylation.
基金supported by the National Natural Science Foundation of China(NO.60927001,60971045)the National Key Program for Developing Basic Research(2010CB933903,2007CB936104)+1 种基金the Chinese 863 High Tech Project(NO.2007AA022007)China National Science and Technology Major Projects(2009ZX10004-311).
文摘Digital microfluidics technology offers a platform for developing diagnostic applications with the advantages of portability,sample and reagent volume reduction,faster analysis,increased automation,low power consumption,compatibility with mass manufacturing and high throughput.In addition to diagnostics,digital microfluidics is finding use in nucleic acid analysis,peptide and protein analysis,cell analysis,drug analysis and delivery and immunization analysis.In this review,we describe these applications,their implementation,and associated design issues.As other review in the digital microfluidics technology,there have been and will be unexpected developments as DMF matures,but we predict that the future is bright for this promising technology at the last section.
文摘Background The non-hemodynamic effects of angiotensin receptor blocker （ARB） in the delay of progression of chronic kidney disease （CKD） remain unclear. In this study, we investigated the influence of irbesartan on the urinary excretion of cytokines in patients with CKD. Methods In this randomized perspective clinical trial, different doses of irbesartan （150 mg/d and 300 mg/d） were given to two groups of patients in a cross-over design. Blood pressure （BP）, creatinine clearance （Ccr） and 24-hour proteinuria were examined. Urinary excretion of cytokines was determined by human inflammatory cytokine antibody array. A two-fold change in spot intensity was considered significant. Results Urinary excretion of cytokines （granulocyte colony stimulating factor （GCSF）, intercellular cell adhesion molecule-1 （ICAM-1）, interferon y （IFN-y）, interleukin 1β （IL-1β）, IL-2, IL-6, IL-8, IL-11, IL-15 and macrophage inflammatory protein 1δ （MIP-Iδ） in group B （irbesartan 300 mg/d） was significantly decreased in comparison to group A （irbesartan 150 mg/d） after 8-week treatment. In group A, 8 weeks of treatment induced a two- to nine-fold reduction in urinary cytokine levels （GCSF, GM-CSF, IFN-γ, IL-1α, IL-11, IL-12p40, MCP-2, MIP-1α）, while increasing the dosage to 300 mg/d further decreased the excretion of GCSF, GM-CSF, IL-12p40, MCP-2 and MIP-1α by week 18. There was no significant difference in BP or Ccr between the two groups. However, 24-hour proteinuria was significantly reduced in both groups, and in group A the reduction was dose dependent.Conclusion Irbesartan offers additional renoprotection in a dose-dependent manner by reducing pro-inflammatory cvtokines excretion in the urine of CKD patients.
文摘Background Neuroblastoma （NB） is one of the most common malignant solid tumors of childhood.It is still not clear whether the apoptosis of tumor cells or the non-tumor cells contributes to the increase of concentration of cytochrome c （Cyt c） in the serum of the cancer patients.The aim of this research was to identify the source of the Cyt c in the serum when the tumor grows up by subcutaneous inoculation of human NB cells into nude mice.Methods We subcutaneously inoculated human NB cells （KP-N-NS） into nude mice and collected the sera of tumor-bearing mice （n=14） and control mice （n=25） 4 weeks later in order to screen for and identify differentially expressed proteins in the serum.Differentially expressed proteins in the serum were screened by surface-enhanced laser desorption/ionization-time-of-fiight （SELDI-TOF） mass spectrometry.Results The relative intensity of a protein having a mass-to-charge ratio （m/z） of 11 609 was 3338.37±3410.85 in the tumor group and 59.84±40.74 in the control group,indicating that the expression level of this protein in the tumor group was 55.8 times higher than that in the control group.Serum proteins were separated and purified by high-performance liquid chromatography （HPLC）.Liquid chromatography coupled with tandem mass spectrometry （LC-MS/MS） was performed to produce peptide mass fingerprints （PMFs）.Spectrum analysis and a database search revealed that the highly expressed protein （m/z=11605.4） from the serum of tumor-bearing mice was the mouse Cyt c.Conclusions Increased concentration of Cyt c in the serum of tumor-bearing nude mice might be partially attributed to the secretion of this protein by non-tumor cells.
