Background Graves＇ ophthalmopathy/orbitopathy （GO） patients often suffer ocular surface damages and tear fluid proteins play a significant role in maintaining healthy ocular surfaces,while changes in tear protein c...Background Graves＇ ophthalmopathy/orbitopathy （GO） patients often suffer ocular surface damages and tear fluid proteins play a significant role in maintaining healthy ocular surfaces,while changes in tear protein components reflect the changes ocular surface abnormalities.In this study proteomics techniques were used to investigate tear protein compositions in GO patients.Methods We carried out a case-control study by comparing tear fluid contents of GO patients with that of healthy subjects.In the first step the tears were subjected to SDS-PAGE electrophoresis and then single protein bands were analyzed by to in-gel trypsin digestion and nano-flow liquid mass spectrometry （LC-MS/MS） using a MS software.Results In tear samples of GO subjects,the protein fractions of inflammation-related protein immunoglobulin kappa chain C region （IgKC） and serum albumin were essentially reduced,whereas a novel isoform of complement component 3 （C3）,which we detected in control subjects,was completely absent in the GO patients＇ tears.Conclusions Reduced protein concentrations of particularly IgKC and complement C3 as well as albumin in the tears of GO patients may contribute to changes in their ocular surfaces via diminished reactive oxygen species （ROS） depletion and adaptive immune responses.The completely absent of C3 in the GO patients＇ tears,may imply that an important inflammatory signaling pathway is affected,which needs further investigation.展开更多
Family identification is helpful for predicting protein functions. It has been known from the literature that longer sequences of base pairs or amino acids are required to study patterns in biological sequences. Since...Family identification is helpful for predicting protein functions. It has been known from the literature that longer sequences of base pairs or amino acids are required to study patterns in biological sequences. Since most protein sequences are relatively short, we randomly concatenate or link the protein sequences from the same family or superfamily together to form longer protein sequences. The 6-letter model, 12-letter model, 20-letter model, the revised Schneider and Wrede scale hydrophobicity, solvent accessibility and stochastic standard state accessibility are used to convert linked protein sequences into numerical sequences. Then multifractal analyses and wavelet analysis are performed on these numerical sequences. The parameters from these analyses can be used to construct parameter spaces where each linked protein is represented by a point. The four classes of proteins, namely the α/β, α＋β and α/β classes, are then distinguished in these parameter spaces. The Fisher linear discriminant algorithm is used to assess the discriminant accuracy. Numerical results indicate that the discriminant accuracies are satisfactory in separating these classes. We find that the linked proteins from the same family or superfamily tend to group together and can be separated from other linked proteins. The methods are helpful for identifying the family of an unknown protein.展开更多
In this study the effects of microwaves on the secondary structure of three typical proteins have been investigated. A set of samples of lysozyme, bovine serum albumin and myoglobin in D2O solutions were exposed for 8...In this study the effects of microwaves on the secondary structure of three typical proteins have been investigated. A set of samples of lysozyme, bovine serum albumin and myoglobin in D2O solutions were exposed for 8 hours to mobile phone microwaves at 900 MHz at a magnetic field intensity around 16 mA/m. The relative effects on the secondary structure of the proteins were studied by means of Fourier Transform Infrared Spectroscopy. An increase of the amide I band intensity in the secondary structure of the proteins was observed after the microwaves exposure. Furthermore, a weak shift of the amide I mode of bovine serum albumin and a heavier shift of the amide I of myoglobin occurred after the exposure. In addition, a clear increasing of the β-sheet components with respect to the α-helix content was observed in the spectra of bovine serum albumin and myoglobin after the exposure, suggesting the hypothesis of the formation of aggregates.展开更多
Terahertz vibrational spectroscopy has recently been demonstrated as a novel noninvasive technique for the characterization of biological molecules. But the interpretation of the experimentally measured terahertz abso...Terahertz vibrational spectroscopy has recently been demonstrated as a novel noninvasive technique for the characterization of biological molecules. But the interpretation of the experimentally measured terahertz absorption bands requires robust computational method. In this paper, we present a statistical method for predicting the absorption peak positions of a macromolecule in the terahertz region. The essence of this method is to calculate the absorption spectra of a biological molecule based on multiple short scale molecular dynamics trajectories instead of using a long time scale trajectory. The method was employed to calculate the absorption peak positions of the protein, thioredoxin from Escherichia coli (E.coli), in the range of 10-25 cm -1 to verify the reliability of this statistical method. The predicted absorption peak positions of thioredoxin show good correlation with measured results demonstrating that the proposed method is effective in terahertz absorption spectra modeling. Such approach can be applied to predict characteristic spectral features of biomolecules in the terahertz region.展开更多
Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization （HACO）, is proposed in this paper to ...Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization （HACO）, is proposed in this paper to tackle continuous-space optimization problems. It was compared with other well-known stochastic methods in the optimization of the benchmark functions and was also used to solve the problem of selecting appropriate dilation efficiently by optimizing the wavelet power spectrum of the hydrophobic sequence of protein, which is the key step on using continuous wavelet transform （CWT） to predict a-helices and connecting peptides.展开更多
In this study, we selected adult normal pituitary gland tissues from six patients during operations for pituitary microadenomas via the transsphenoidal approach for extended normal pituitary tissue resection around th...In this study, we selected adult normal pituitary gland tissues from six patients during operations for pituitary microadenomas via the transsphenoidal approach for extended normal pituitary tissue resection around the tumor, and analyzed the protein expression of human normal pituitary using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry proteomics technology. The ten most highly expressed proteins in normal human pituitary were： alpha 3 type VI collagen isoform 5 precursor （abundance among tall pituitary proteins 1.30%）, fibrinogen beta chain preproprotein （0.99%）, vimentin （0.73%）, prolactin （0.69%）, ATP synthase, H~ transporting and mitochondrial F1 complex beta subunit precursor （0.52%）, keratin I （0.49%）, growth hormone （0.45%）, carbonic anhydrase I （0.40%）, heat shock protein 90 kDa I （0.31%）, and annexin V （0.30%）. Based on the biological function classifications of these proteins, the top three categories by content were neuroendocrine proteins （abundance among all pituitary proteins, 40.1%）, catalytic and metabolic proteins （28.3%）, and cell signal transduction proteins （9.8%）. Based on cell positioning classification, the top three categories were cell organelle （24.5%） membrane （20.8%）, and cytoplasm （13.0%）. Based on biological process classification, the top three categories of proteins are involved in physiological processes （42.9%）, cellular processes （40.4%）, and regulation of biological processes （9.1%）. Our experimental findings indicate that a protein expression profile database of normal human pituitary can be precisely and efficiently established by proteomics technology.展开更多
Elucidating the initial kinetics of folding pathways is critical to the understanding of the protein folding mechanism. Transient infrared spectroscopy has proved a powerful tool to probe the folding kinetics. Herein ...Elucidating the initial kinetics of folding pathways is critical to the understanding of the protein folding mechanism. Transient infrared spectroscopy has proved a powerful tool to probe the folding kinetics. Herein we report the construction of a nanosecond laser-induced temperature-jump （T-jump） technique coupled to a nanosecond timeresolved transient mid-infrared （mid-IR） spectrometer system capable of investigating the protein folding kinetics with a temporal resolution of 50 ns after deconvolution of the instrumental response function. The mid-IR source is a liquid N2 cooled CO laser covering a spectral range of 5.0μm （2000 cm^-1）-6.5μm （1540 cm^-1）. The heating pulse was generated by a high pressure H2 Raman shifter at wavelength of 1.9μm. The maximum temperature-jump could reach as high as 26±1℃. The fast folding/unfolding dynamics of cytochrome C was investigated by the constructed system, providing an example.展开更多
The contactin-associated protein （Caspr） family participates in nerve excitation and conduction, and neurotransmitter release in myelinated axons. We analyzed the structures and functions of the Caspr family- CNTNA...The contactin-associated protein （Caspr） family participates in nerve excitation and conduction, and neurotransmitter release in myelinated axons. We analyzed the structures and functions of the Caspr family- CNTNAP1 （Casprl）, CNTNAP2 （Caspr2）, CNTNAP3 （Caspr3）, CNTNAP4 （Caspr4） and CNTNAP5 （Caspr5）, Casprl-5 is not only involved in the formation of myelinated axons, but also participates in maintaining the stability of adjacent connections. Casprl participates in the formation, differentiation, and proliferation of neurons and astrocytes, and in motor control and cognitive function. We also analyzed the relationship between the Caspr family and neurodegenerative diseases, multiple sclerosis, and autoimmune encephalitis. However, the effects of Caspr on disease course and prognosis remain poorly understood. The effects of Caspr on disease diagnosis and treatment need further investigation.展开更多
由条形柄锈菌小麦专化型Puccinia striiformis f. sp.tritici(Pst)引起的条锈病,长期严重威胁小麦安全生产。Pst通过毒性变异产生新毒性小种或致病类型,能克服生产上已应用的抗病基因,导致抗病品种感病。因此,挖掘抗条锈病基因资源对小...由条形柄锈菌小麦专化型Puccinia striiformis f. sp.tritici(Pst)引起的条锈病,长期严重威胁小麦安全生产。Pst通过毒性变异产生新毒性小种或致病类型,能克服生产上已应用的抗病基因,导致抗病品种感病。因此,挖掘抗条锈病基因资源对小麦抗病遗传改良和加快抗病新品种培育具有重要意义。蛋白激酶在应答病原菌侵染,传递植物免疫信号中发挥重要作用。本研究通过小麦转录组数据分析,筛选到参与应答Pst、小麦白粉菌Blumeria graminis f. sp.tritici和赤霉病菌Fusarium graminearum侵染的蛋白激酶基因TaPiPK1。该蛋白激酶基因编码551个氨基酸,C末端含有一个STK激酶结构域。利用RT-qPCR检测发现,TaPiPK1在小麦与条锈菌非亲和互作的前期上调表达;TaPiPK1主要定位于细胞质与细胞膜。利用大麦条纹花叶病毒介导的基因沉默技术(BSMV-VIGS)瞬时沉默TaPiPK1,显著降低小麦‘水源11’对条锈菌非亲和小种CYR23的抗性,表明TaPiPK1参与小麦抗条锈病反应并发挥重要作用。因此,TaPiPK1有可能作为潜在的基因资源用于小麦抗条锈病育种。展开更多
【目的】建立棉花毛籽蛋白质和油分含量的近红外检测校正模型。【方法】检测样本的蛋白质含量和油分含量,根据光谱-理化值共生距离算法(sample set partitioning based on joint X-Y distance sampling,SPXY)按照3∶1的比例将426个样本...【目的】建立棉花毛籽蛋白质和油分含量的近红外检测校正模型。【方法】检测样本的蛋白质含量和油分含量,根据光谱-理化值共生距离算法(sample set partitioning based on joint X-Y distance sampling,SPXY)按照3∶1的比例将426个样本划分为包含320个样本的校正集和106个样本的预测集,结合多元散射校正和一阶导数等光谱预处理方法对模型进行优化,并采用线性偏最小二乘法(partial least square method,PLS)、支持向量机(support vector machine,SVM)和随机森林(random forest,RF)3种方法对比分析建立棉花毛籽蛋白质和油分含量的近红外快速测定模型,以决定系数、均方根误差和剩余预测偏差作为模型的评价指标。【结果】SVM模型和PLS模型在校正集的拟合效果较好,决定系数均大于0.8,但对预测集的拟合决定系数不到0.8,说明模型均存在过拟合现象;而RF模型在校正集和预测集的拟合效果都非常好,决定系数均大于0.9,其中蛋白质含量预测模型的决定系数、预测均方根误差和剩余预测偏差分别为0.9459、0.9352和4.5391,油分含量预测模型的决定系数、预测均方根误差和剩余预测偏差分别为0.9097、0.7704和3.4891。【结论】基于RF方法建立的预测模型能较好地应用于基于近红外光谱的棉花毛籽的蛋白质含量和油分含量检测,并可代替化学测定方法。研究结果不仅为棉花种子品质育种、棉籽加工生产和销售中棉籽营养品质的快速、无损评价奠定了基础,并可为其他作物种子的无损分析提供技术借鉴。展开更多
文摘Background Graves＇ ophthalmopathy/orbitopathy （GO） patients often suffer ocular surface damages and tear fluid proteins play a significant role in maintaining healthy ocular surfaces,while changes in tear protein components reflect the changes ocular surface abnormalities.In this study proteomics techniques were used to investigate tear protein compositions in GO patients.Methods We carried out a case-control study by comparing tear fluid contents of GO patients with that of healthy subjects.In the first step the tears were subjected to SDS-PAGE electrophoresis and then single protein bands were analyzed by to in-gel trypsin digestion and nano-flow liquid mass spectrometry （LC-MS/MS） using a MS software.Results In tear samples of GO subjects,the protein fractions of inflammation-related protein immunoglobulin kappa chain C region （IgKC） and serum albumin were essentially reduced,whereas a novel isoform of complement component 3 （C3）,which we detected in control subjects,was completely absent in the GO patients＇ tears.Conclusions Reduced protein concentrations of particularly IgKC and complement C3 as well as albumin in the tears of GO patients may contribute to changes in their ocular surfaces via diminished reactive oxygen species （ROS） depletion and adaptive immune responses.The completely absent of C3 in the GO patients＇ tears,may imply that an important inflammatory signaling pathway is affected,which needs further investigation.
基金Project supported by the Australian Research Council(Grant No.DP0559807)a Research Capacity Building Award at QUT,Scientific Research Fund of Hunan Provincial Education Department of China(Grant No.06C826)+3 种基金the Chinese Program for New Century Excellent Talents in University(Grant No.NCET-08-06867)the Hunan Provincial Natural Science Foundation of China(Grant No.10JJ7001)the Program for Furong Scholars of Hunan Province of Chinathe Aid program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province of China
文摘Family identification is helpful for predicting protein functions. It has been known from the literature that longer sequences of base pairs or amino acids are required to study patterns in biological sequences. Since most protein sequences are relatively short, we randomly concatenate or link the protein sequences from the same family or superfamily together to form longer protein sequences. The 6-letter model, 12-letter model, 20-letter model, the revised Schneider and Wrede scale hydrophobicity, solvent accessibility and stochastic standard state accessibility are used to convert linked protein sequences into numerical sequences. Then multifractal analyses and wavelet analysis are performed on these numerical sequences. The parameters from these analyses can be used to construct parameter spaces where each linked protein is represented by a point. The four classes of proteins, namely the α/β, α＋β and α/β classes, are then distinguished in these parameter spaces. The Fisher linear discriminant algorithm is used to assess the discriminant accuracy. Numerical results indicate that the discriminant accuracies are satisfactory in separating these classes. We find that the linked proteins from the same family or superfamily tend to group together and can be separated from other linked proteins. The methods are helpful for identifying the family of an unknown protein.
文摘In this study the effects of microwaves on the secondary structure of three typical proteins have been investigated. A set of samples of lysozyme, bovine serum albumin and myoglobin in D2O solutions were exposed for 8 hours to mobile phone microwaves at 900 MHz at a magnetic field intensity around 16 mA/m. The relative effects on the secondary structure of the proteins were studied by means of Fourier Transform Infrared Spectroscopy. An increase of the amide I band intensity in the secondary structure of the proteins was observed after the microwaves exposure. Furthermore, a weak shift of the amide I mode of bovine serum albumin and a heavier shift of the amide I of myoglobin occurred after the exposure. In addition, a clear increasing of the β-sheet components with respect to the α-helix content was observed in the spectra of bovine serum albumin and myoglobin after the exposure, suggesting the hypothesis of the formation of aggregates.
基金Supported by National Science Foundation of China(Nos.60907044,91027020 and 11005148)
文摘Terahertz vibrational spectroscopy has recently been demonstrated as a novel noninvasive technique for the characterization of biological molecules. But the interpretation of the experimentally measured terahertz absorption bands requires robust computational method. In this paper, we present a statistical method for predicting the absorption peak positions of a macromolecule in the terahertz region. The essence of this method is to calculate the absorption spectra of a biological molecule based on multiple short scale molecular dynamics trajectories instead of using a long time scale trajectory. The method was employed to calculate the absorption peak positions of the protein, thioredoxin from Escherichia coli (E.coli), in the range of 10-25 cm -1 to verify the reliability of this statistical method. The predicted absorption peak positions of thioredoxin show good correlation with measured results demonstrating that the proposed method is effective in terahertz absorption spectra modeling. Such approach can be applied to predict characteristic spectral features of biomolecules in the terahertz region.
基金the National Natural Science Foundation of China(No.20475068) the Guangdong Provincial Natural Science Foundation(No.031577).
文摘Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization （HACO）, is proposed in this paper to tackle continuous-space optimization problems. It was compared with other well-known stochastic methods in the optimization of the benchmark functions and was also used to solve the problem of selecting appropriate dilation efficiently by optimizing the wavelet power spectrum of the hydrophobic sequence of protein, which is the key step on using continuous wavelet transform （CWT） to predict a-helices and connecting peptides.
基金supported by the National NaturalScience Foundation of China, No. 81200890
文摘In this study, we selected adult normal pituitary gland tissues from six patients during operations for pituitary microadenomas via the transsphenoidal approach for extended normal pituitary tissue resection around the tumor, and analyzed the protein expression of human normal pituitary using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry proteomics technology. The ten most highly expressed proteins in normal human pituitary were： alpha 3 type VI collagen isoform 5 precursor （abundance among tall pituitary proteins 1.30%）, fibrinogen beta chain preproprotein （0.99%）, vimentin （0.73%）, prolactin （0.69%）, ATP synthase, H~ transporting and mitochondrial F1 complex beta subunit precursor （0.52%）, keratin I （0.49%）, growth hormone （0.45%）, carbonic anhydrase I （0.40%）, heat shock protein 90 kDa I （0.31%）, and annexin V （0.30%）. Based on the biological function classifications of these proteins, the top three categories by content were neuroendocrine proteins （abundance among all pituitary proteins, 40.1%）, catalytic and metabolic proteins （28.3%）, and cell signal transduction proteins （9.8%）. Based on cell positioning classification, the top three categories were cell organelle （24.5%） membrane （20.8%）, and cytoplasm （13.0%）. Based on biological process classification, the top three categories of proteins are involved in physiological processes （42.9%）, cellular processes （40.4%）, and regulation of biological processes （9.1%）. Our experimental findings indicate that a protein expression profile database of normal human pituitary can be precisely and efficiently established by proteomics technology.
基金Project supported by the National Natural Science Foundation of China （Grant No 20373088） and Program for innovation group （Grant No 60321002）.
文摘Elucidating the initial kinetics of folding pathways is critical to the understanding of the protein folding mechanism. Transient infrared spectroscopy has proved a powerful tool to probe the folding kinetics. Herein we report the construction of a nanosecond laser-induced temperature-jump （T-jump） technique coupled to a nanosecond timeresolved transient mid-infrared （mid-IR） spectrometer system capable of investigating the protein folding kinetics with a temporal resolution of 50 ns after deconvolution of the instrumental response function. The mid-IR source is a liquid N2 cooled CO laser covering a spectral range of 5.0μm （2000 cm^-1）-6.5μm （1540 cm^-1）. The heating pulse was generated by a high pressure H2 Raman shifter at wavelength of 1.9μm. The maximum temperature-jump could reach as high as 26±1℃. The fast folding/unfolding dynamics of cytochrome C was investigated by the constructed system, providing an example.
基金supported by a grant from the Instructional Program of Science and Technology Bureau of Wuxi City of China,No.0302B010507130039PB
文摘The contactin-associated protein （Caspr） family participates in nerve excitation and conduction, and neurotransmitter release in myelinated axons. We analyzed the structures and functions of the Caspr family- CNTNAP1 （Casprl）, CNTNAP2 （Caspr2）, CNTNAP3 （Caspr3）, CNTNAP4 （Caspr4） and CNTNAP5 （Caspr5）, Casprl-5 is not only involved in the formation of myelinated axons, but also participates in maintaining the stability of adjacent connections. Casprl participates in the formation, differentiation, and proliferation of neurons and astrocytes, and in motor control and cognitive function. We also analyzed the relationship between the Caspr family and neurodegenerative diseases, multiple sclerosis, and autoimmune encephalitis. However, the effects of Caspr on disease course and prognosis remain poorly understood. The effects of Caspr on disease diagnosis and treatment need further investigation.
文摘由条形柄锈菌小麦专化型Puccinia striiformis f. sp.tritici(Pst)引起的条锈病,长期严重威胁小麦安全生产。Pst通过毒性变异产生新毒性小种或致病类型,能克服生产上已应用的抗病基因,导致抗病品种感病。因此,挖掘抗条锈病基因资源对小麦抗病遗传改良和加快抗病新品种培育具有重要意义。蛋白激酶在应答病原菌侵染,传递植物免疫信号中发挥重要作用。本研究通过小麦转录组数据分析,筛选到参与应答Pst、小麦白粉菌Blumeria graminis f. sp.tritici和赤霉病菌Fusarium graminearum侵染的蛋白激酶基因TaPiPK1。该蛋白激酶基因编码551个氨基酸,C末端含有一个STK激酶结构域。利用RT-qPCR检测发现,TaPiPK1在小麦与条锈菌非亲和互作的前期上调表达;TaPiPK1主要定位于细胞质与细胞膜。利用大麦条纹花叶病毒介导的基因沉默技术(BSMV-VIGS)瞬时沉默TaPiPK1,显著降低小麦‘水源11’对条锈菌非亲和小种CYR23的抗性,表明TaPiPK1参与小麦抗条锈病反应并发挥重要作用。因此,TaPiPK1有可能作为潜在的基因资源用于小麦抗条锈病育种。
文摘【目的】建立棉花毛籽蛋白质和油分含量的近红外检测校正模型。【方法】检测样本的蛋白质含量和油分含量,根据光谱-理化值共生距离算法(sample set partitioning based on joint X-Y distance sampling,SPXY)按照3∶1的比例将426个样本划分为包含320个样本的校正集和106个样本的预测集,结合多元散射校正和一阶导数等光谱预处理方法对模型进行优化,并采用线性偏最小二乘法(partial least square method,PLS)、支持向量机(support vector machine,SVM)和随机森林(random forest,RF)3种方法对比分析建立棉花毛籽蛋白质和油分含量的近红外快速测定模型,以决定系数、均方根误差和剩余预测偏差作为模型的评价指标。【结果】SVM模型和PLS模型在校正集的拟合效果较好,决定系数均大于0.8,但对预测集的拟合决定系数不到0.8,说明模型均存在过拟合现象;而RF模型在校正集和预测集的拟合效果都非常好,决定系数均大于0.9,其中蛋白质含量预测模型的决定系数、预测均方根误差和剩余预测偏差分别为0.9459、0.9352和4.5391,油分含量预测模型的决定系数、预测均方根误差和剩余预测偏差分别为0.9097、0.7704和3.4891。【结论】基于RF方法建立的预测模型能较好地应用于基于近红外光谱的棉花毛籽的蛋白质含量和油分含量检测,并可代替化学测定方法。研究结果不仅为棉花种子品质育种、棉籽加工生产和销售中棉籽营养品质的快速、无损评价奠定了基础,并可为其他作物种子的无损分析提供技术借鉴。
