Detection of C′,C<Superscript>α</Superscript> correlations in proteins using a new time- and sensitivity-optimal experiment

Sensitivity- and time-optimal experiment, called COCAINE (CO-CA In- and aNtiphase spectra with sensitivity Enhancement), is proposed to correlate chemical shifts of ¹³C and ¹³C spins in proteins. A comparison of the sensitivity and duration of the experiment with the corresponding theoretical unitary bounds shows that the COCAINE experiment achieves maximum possible transfer efficiency in the shortest possible time, and in this sense the sequence is optimal. Compared to the standard HSQC, the COCAINE experiment delivers a 2.7-fold gain in sensitivity. This newly proposed experiment can be used for assignment of backbone resonances in large deuterated proteins effectively bridging ¹³C and ¹³C resonances in adjacent amino acids. Due to the spin-state selection employed, the COCAINE experiment can also be used for efficient measurements of one-bond couplings (e.g. scalar and residual dipolar couplings) in any two-spin system (e.g. the N/H in the backbone of protein).     

Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex

Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%–30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T₁, T₂, and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature.     

Measuring the fit of sequence data to phylogenetic model: allowing for missing data

It is fundamentally important to assess the fit of data to model in phylogenetic and evolutionary studies. Phylogenetic methods using molecular sequences typically start with a multiple alignment. It is possible to measure the fit of data to model expectations of data, for example, via the likelihood-ratio (G) test or the X(2) test, if all sites in all sequences have an unambiguous residue. However, nearly all alignments of interest contain sites (columns of the alignment) with missing data, that is, ambiguous nucleotides, gaps, or unsequenced regions, which must presently be removed before using the above tests. Unfortunately, this is often either undesirable or impractical, as it will discard much of the data. Here, we show how iterative ML estimators may directly estimate the site-pattern probabilities for columns with missing data, given only standard i.i.d. assumptions. The optimization may use an EM or Newton algorithm, or any other hill-climbing approach. The resulting optimal likelihood under the unconstrained or multinomial model may be compared directly with the likelihood of the data coming from the model (a G statistic). Alternatively the modified observed and the expected frequencies of site patterns may be compared using a X(2) test. The distribution of such statistics is best assessed using appropriate simulations. The new method is applicable to models using codons or paired sites. The methods are also useful with Hadamard conjugations (spectral analysis) and are illustrated with these and with ML evolutionary models that allow site-rate variability.     

Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families

We investigate the performance of combinatorial pattern discovery to detect remote sequence similarities in terms of both biological accuracy and computational efficiency for a pair of distantly related families, as a case study. The two families represent the cupredoxins and multicopper oxidases, both containing blue copper-binding domains. These families present a challenging case due to low sequence similarity, different local structure, and variable sequence conservation at their copper-binding active sites. In this study, we investigate a new approach for automatically identifying weak sequence similarities that is based on combinatorial pattern discovery. We compare its performance with a traditional, HMM-based scheme and obtain estimates for sensitivity and specificity of the two approaches. Our analysis suggests that pattern discovery methods can be substantially more sensitive in detecting remote protein relationships while at the same time guaranteeing high specificity.     

High-resolution time series of vessel density in Kenyan mangrove trees reveal a link with climate

Tropical trees are often excluded from dendrochronological investigations because of a lack of distinct growth ring boundaries, causing a gap in paleoclimate reconstructions from tropical regions. The potential use of time series of vessel features (density, diameter, surface area and hydraulic conductivity) combined with spectral analysis as a proxy for environmental conditions in the mangrove Rhizophora mucronata was investigated. Intra-annual differences in the vessel features revealed a trade-off between hydraulic efficiency (large vessels) during the rainy season and hydraulic safety (small, more numerous vessels) during the dry season. In addition to the earlywood-latewood variations, a semiannual signal was discovered in the vessel density and diameters after Fourier transformation. The similarity in the Fourier spectra of the vessel features and the climate data, in particular mean relative humidity and precipitation, provides strong evidence for a climatic driving force for the intra-annual variability of the vessel features. The high-resolution approach used in this study, in combination with spectral analysis, may have great potential for the study of climate variability in tropical regions.     

鲫鱼外层视网膜突触强度可塑性及模型分析

视网膜亮型水平细胞的光谱敏感性随刺激模式而变,建立一数学模型以对这种现象的生理机制进行探讨。模型包括两个并行的信号通道,即红敏视锥和绿敏视锥信号通道,神经元之间的突触连接强度在模型中表示为相应通道的的放大系统;系统输出,即水平细胞对光反应幅度,为由两个通道输出之线性和。模型假设各个通道的状态是可调的,其各个时刻的放大系数与其自身状态态呈正相关,而与系统输出呈负相关。模型输出能对实验数据做出较好的描述。     

Differing sensitivity of tumor cells to apoptosis induced by iron deprivation in vitro

We studied the sensitivity of tumor cells to the induction of apoptosis by iron deprivation. Iron deprivation was achieved by the employment of a defined iron-deficient culture medium. Mouse 38C13 cells and human Raji cells die within 48 and 96 h of incubation in iron-deficient medium, respectively. On the contrary, mouse EL4 cells and human HeLa cells are completely resistant to the induction of death under the same experimental arrangement. Deoxyribonucleic acid fragmentation analysis by agarose gel electrophoresis as well as flow cytometric analysis after propidium iodide staining detected in 38C13 and Raji cells, but not in EL4 and HeLa cells, changes characteristic to apoptosis. The 38C13 cells, sensitive to iron deprivation, also displayed a similar degree of sensitivity to apoptosis induction by thiol deprivation (achieved by 2-mercaptoethanol withdrawal from the culture medium) as well as by rotenone (50 nM), hydroxyurea (50 microM), methotrexate (20 nM), and doxorubicin (100 nM). Raji cells shared with 38C13 cells a sensitivity to rotenone, methotrexate, doxorubicin, and, to a certain degree, to hydroxyurea. However, Raji cells were completely resistant to thiol deprivation. EI4 and HeLa cells, resistant to iron deprivation, also displayed a greater degree of resistance to most of the other apoptotic stimuli than did their sensitive counterparts. We conclude that some tumor cells in vitro are sensitive to apoptosis induction by iron deprivation, while other tumor cells are resistant. All the tumors found to be sensitive to iron deprivation in this study (four cell lines) are of hematopoietic origin. The mechanism of resistance to apoptosis induction by iron deprivation differs from the mechanism of resistance to thiol deprivation.     

EEG Spectral Analysis of Relaxation Techniques

The acute central nervous system effects of relaxation techniques (RT) have not been systematically studied. We conducted a controlled, randomized study of the central nervous system effects of RT using spectral analysis of EEG activity. Thirty-six subjects were randomized to either RT or a music comparison condition. After listening to an RT audiotape or music audiotapes daily for 6 weeks, the acute central nervous system effects of RT and music were measured using power spectral analysis of alpha and theta EEG activity in all cortical regions. RT produced significantly greater increases in theta activity in multiple cortical regions compared to the music condition. These findings are consistent with widespread reductions in cortical arousal during RT. They extend previous findings and suggest that theta, and not alpha, EEG may be the most reliable marker of the central nervous system effects of RT. These findings demonstrate that RT produce greater reductions in central nervous system activity than a credible comparison condition. The findings suggest that RT represent a hypoactive central nervous system state that may be similar to Stage 1 sleep and that RT may exert their therapeutic effects, in part, through cerebral energy conservation/restoration.     

Sympathetic denervation-induced changes in G protein expression in enteric neurons of the guinea pig colon

Chronic sympathetic denervation entails subsensitivity to alpha(2)-adrenoceptor agonists and supersensitivity to kappa- and mu-opioid receptor agonists modulating cholinergic neurons in the guinea pig colon. A possible role for signal transduction G proteins in contributing to development of these sensitivity changes was investigated. Pertussis toxin (PTX), a blocker of the G(i/o)-type family of G proteins significantly reduced the inhibitory effects of UK14,304 (alpha(2)-adrenoceptor agonist), U69593 (kappa-opioid receptor agonist) and DAMGO (mu-opioid receptor agonist) on acetylcholine (ACh) overflow in preparations obtained from normal animals, but not in those obtained from sympathetically denervated animals. In this experimental condition, immunoblot analysis revealed reduced levels of G(alphao), G(alphai2), G(alphai3) and G(beta) in myenteric plexus synaptosomes. On reverse, synaptosomal levels of G(alphai1) and G(alphaz), a PTX-insensitive G-protein, increased after chronic ablation of the sympathetic pathways. These data suggest that changes in the function and expression of inhibitory G proteins coupled to alpha(2)-adrenoceptors, kappa- and mu-opioid receptors occur in the myenteric plexus of the guinea pig colon after chronic sympathetic denervation. The possibility that regulation of G proteins represents one of the biochemical mechanisms at the basis of the changes in sensitivity of enteric cholinergic neurons to alpha(2)-adrenoceptor, kappa- and mu-opioid receptor agonists is discussed.