Evaluation of the jackknife technique for fitting multiexponential functions to biochemical data

The jackknife technique was tested by fitting a two-exponential function to the time course of disappearance of radioactivity from the area of a wheat leaf that had been fed ¹⁴CO₂. The function was fitted by both unweighted and weighted least squares, first without and then with the jackknife. Weighting altered the estimates of the function's parameters, but jackknifing did not. Hence jackknifing did not remove any of the bias introduced by incorrect weighting. The confidence limits of the parameters calculated by jackknifing were greater than those estimated from the variance-covariance matrix of the regression, but similar to those derived from replicate experiments. The jackknife also allowed confidence limits for the rate constants and transit time of the underlying two-compartment model to be derived.     

Mapping functions

Accurate estimation of map distance between markers is important for the construction of large-scale linkage maps because it provides reliable and useful linkage information of markers on chromosomes. How to improve accuracy of estimating map distances depends on an appropriate mapping function. We used the coefficient of coincidence to integrate the Haldane function, in which crossovers are assumed to be independent and the Morgan function, in which crossovers are assumed to be interfered, and produce a new mapping function. The mapping function based on positive interference is referred to as the positive function and that on negative interference as the negative function. In these two mapping functions, map distances between loci are determined by both recombination frequencies and the coefficient of coincidence. We applied our mapping functions to four examples and show that our map estimates have much higher goodness-of-fit to the observed mapping data than the Haldane and Kosambi functions. Therefore, they can provide much more precise estimates of map distances than the two conventional mapping functions. Furthermore, our mapping functions produced almost linear (additive) map distances.     

Analysis of exponential decay curves: a three-step scheme for computing exponents

A study of four techniques is examined to determine which method has the greater overall utility. An iterative least-squares error minimization method provides the greatest accuracy, while a linear algebraic method is accurate only for two-exponential data with small error. Consequently, a three-method sequential identification scheme is devised utilizing a graphical method, a transform method, and an iterative method. This scheme is successfully applied to physiological data containing three and four exponents.     

Non-canonical functions of the cellular transporter P-glycoprotein

P-glycoprotein/ABCB1 (Pgp) is a well known protein of cell defense system. It is localized in cell membrane and pumps different drugs out of various cells using ATP energy. Its overexpression is associated with the development of multidrug resistance (MDR) in cancer cells. The data showing that Pgp also has other functions appeared recently, and this review surveys these data. In particular, (1) Pgp can protect cells from apoptosis; it suppresses the expression of endogenous protein TRAIL and decreases the activity of caspases 8 and 3; (2) Pgp is able to act as an outwardly directed flippase; (3) Pgp participates in a proper development of the innate immune response to intracellular pathogens and in the development of inflammation; (4) functionally active Pgp can be transferred from drug-resistant to drug-sensitive cells by microvesicles (MV). This is a new way of the Pgp-mediated MDR emergence in populations of tumor cells. Thus, Pgp functions as a regulator of some cellular processes. Molecular mechanisms of the Pgp influence on tumor cell viability are related not only with the drug efflux but also with some other functions.     

Adrenergic modulation of the delayed rectifier potassium channel in calf cardiac Purkinje fibers.

We have investigated the modulation of the delayed rectifier potassium channel in calf cardiac Purkinje fibers by the neurohormone norepinephrine. We find that 0.5 microM norepinephrine increases this K channel current by a factor of 2.7. A maximal increase of about four was found for concentrations of 1 microM and above. Norepinephrine produced a small (less than 5 mV) and variable shift of the K channel reversal potential toward more negative values. The kinetics of the potassium channel are well described by a two-exponential process, both in the absence and presence of norepinephrine. However, norepinephrine substantially decreases the slower time constant with no significant effect on the fast time constant. Potassium channel activation curves in the presence of norepinephrine are very similar to control curves except at large positive potentials. A simple sequential three-state model for this channel can reproduce these data both with and without norepinephrine. The logarithms of the rate constants derived from this model are quadratic functions of voltage, suggesting the involvement of electric field-induced dipoles in the gating of this channel. Most of the kinetic effects of norepinephrine appear to be on a single rate constant.     

Chain functions and scoring functions in genetic networks

One of the grand challenges of system biology is to reconstruct the network of regulatory control among genes and proteins. High throughput data, particularly from expression experiments, may gradually make this possible in the future. Here we address two key ingredients in any such 'reverse engineering' effort: The choice of a biologically relevant, yet restricted, set of potential regulation functions, and the appropriate score to evaluate candidate regulatory relations. We propose a set of regulation functions which we call chain functions, and argue for their ubiquity in biological networks. We analyze their complexity and show that their number is exponentially smaller than all boolean functions of the same dimension. We define two new scores: one evaluating the fitness of a candidate set of regulators of a particular gene, and the other evaluating a candidate function. Both scores use established statistical methods. Finally, we test our methods on experimental gene expression data from the yeast galactose pathway. We show the utility of using chain functions and the improved inference using our scores in comparison to several extant scores. We demonstrate that the combined use of the two scores gives an extra advantage. We expect both chain functions and the new scores to be helpful in future attempts to infer regulatory networks.     

卵泡抑素相关蛋白的病理生理功能

卵泡抑素相关蛋白(follistatin related protein,FRP)是一种细胞外基质糖蛋白,该蛋白参与细胞增殖、迁移、组织重塑、胚胎发育、细胞间相互作用及多种病理生理过程.近年研究显示,该蛋白同时具有抑制细胞凋亡和抑制细胞增殖的双重功能:在心肌缺血的动物模型中,FRP被证实有保护心肌细胞、抗凋亡、促进内皮细胞增殖等功能;FRP也可由血管平滑肌细胞合成分泌,并具有反馈调节平滑肌细胞功能的作用,该蛋白还可抑制多种肿瘤细胞增殖.     

Non-canonical functions of RGS proteins

Regulators of G protein signalling (RGS) proteins are united into a family by the presence of the RGS domain which serves as a GTPase-activating protein (GAP) for various Galpha subunits of heterotrimeric G proteins. Through this mechanism, RGS proteins regulate signalling of numerous G protein-coupled receptors. In addition to the RGS domains, RGS proteins contain diverse regions of various lengths that regulate intracellular localization, GAP activity or receptor selectivity of RGS proteins, often through interaction with other partners. However, it is becoming increasingly appreciated that through these non-RGS regions, RGS proteins can serve non-canonical functions distinct from inactivation of Galpha subunits. This review summarizes the data implicating RGS proteins in the (i) regulation of G protein signalling by non-canonical mechanisms, (ii) regulation of non-G protein signalling, (iii) signal transduction from receptors not coupled to G proteins, (iv) activation of mitogen-activated protein kinases, and (v) non-canonical functions in the nucleus.     

Structure and functions of bacterial proteinase precursors

The data on the precursors of bacterial proteases were generalized. The structure and special features of processing of the precursors of bacillary subtilisins, the alpha-lytic protease from Lysobacter enzymogenes and the related chymotrypsin-like proteases from Streptomyces griseus, and the metalloproteases from bacilli and Pseudomonas aeruginosa were discussed. The approaches to producing the precursors and the protease propeptides and to in vitro characterizing them were particularly analyzed. The following physiological functions of the propeptides within the protease precursors were considered probable: (a) inhibition of the proteases to protect the host cells from the proteolytic damage; (b) participation in the folding of the mature enzyme; and (c) providing for the protease interaction with the bacterial cell surveillance mechanisms, including protease translocation through the cell wall.     

Biological functions of carotenoids--diversity and evolution

Carotenoids first emerged in archaebacteria as lipids reinforcing cell membranes. To serve this function their long molecules have extremely rigid backbone due to the linear chain of usually 10 to 11 conjugated C=C bonds in transconfiguration--the length corresponding the thickness of hydrophobic zone of membrane which they penetrate as "molecular rivets". Carotenoids retain their membrane-reinforcing function in some fungi and animals. The general structure of carotenoid molecule, originally having evolved for mechanical functions in membranes, possess a number of other properties that were later used for independent functions. The most striking fact is that these properties proved to fit some new functions to perfection. The polyene chain of 9-11 double bonds absorbs light precisely in the gap of chlorophyll absorption--function as accessory light-harvesting pigments in all plants; Unique arrangement of electronic levels owing to the by polyene chain structure makes carotenoids the only natural compounds capable of excitation energy transfer both (i) from carotenoid excited state to chlorophyll in the light-harvesting complex and (ii) from triplet chlorophyll or singlet oxygen to carotenoid in photosynthetic reaction centers--protection of RC from photodamage. The linear system of conjugated C=C bonds provides high reducing potential of carotenoid molecules making them potent antioxidants in lipid formations. Still, there is a lack of evidence of the chemical antioxidant function of carotenoids, especially in higher organisms; most data demonstrate an antioxidant ability rather than a function. Carotenoids have many other independent biological functions, including: specific coloration patterns in plants and animals, screening from excessive light and spectral filtering, defense of egg proteins from proteases in some invertebrates; the direct carotenoid derivative--retinal--acts as visual pigment in all animals and as chromophore in bacteriorhodopsin photosynthesis, retinoic acid in animals and abscisic acid in plants serve as hormones. All these functions utilize various properties (mechanical, electronic, stereospecific) of a single structure evolved in bacteria for a single membrane-reinforcing function, thus demonstrating an example of pure evolutionary preadaptation. One of the practical conclusions that can be reached by reviewing uniquely diverse properties and functions of carotenoids is that, when considering possible mechanisms of their effects in organisms (e.g., anticarcinogenic action), all their functional traits should be taken into account.     

Predicting protein functions from PPI networks using functional aggregation

Predicting protein functions computationally from massive protein-protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method.     

Risk functions and expected spike density functions for neurons in the cat cochlear nucleus

The temporal properties of spontaneous and (or) evoked discharges of 157 neurons localized in dorsal cochlear nucleus of anaesthetized cats have been studied. Tone bursts were presented at stimulus best frequency in a free field from the side of ipsilateral ear. About half of cells were characterized by paused or build-up types of the discharge. For all such units a long lasting post-spike decrease in excitability could be seen from the analysis of hazard functions of spontaneous and evoked activity. As a result, the time dependence of conditional probability of the first crossing of the threshold (under condition of an absence of previous response spikes) or expecting probability function (EPF) were over the usual peristimulus histograms. Units with chopper discharges usually did not demonstrate alternative peaks in EPF. We interpreted this fact as evidence that chopper discharge pattern is a result of strong post spike decrease in excitability. Such pattern doesn't demonstrate an existence of real periodicity of the unit. In primary-like units the hazard functions demonstrated only minor after-spike decrease of excitability, and the EPFs were similar to the initial part of peristimulus histograms. Type II units (presumably inhibitory cells) were characterized by non-monotonous hazard functions and by a tendency to burst response patterns. In some cells, we observed a tendency to existence of real intrinsic oscillations both in the EPFs and hazard functions.     

Isotype-specific functions of Raf kinases

The family of Raf-protein kinases consisting of A-Raf, B-Raf, and c-Raf-1 is involved in cellular processes which regulate proliferation, differentiation, and apoptosis. Cell-culture experiments and the knockout of individual Raf genes suggested that the three Raf isoforms have overlapping and unique regulatory functions. However, it is not known how these isotype-specific functions of Raf kinases occur in the cell. Published data suggest that Raf proteins might differ in the regulation of their activation as well as in their ability to connect to downstream signaling pathways. Since Raf is part of a multiprotein complex and protein-protein interactions are important for Raf signaling, we propose that isotype-specific functions can be achieved by isotype-restricted protein binding. Recently we were able to identify candidates for such Raf-isoform-specific interaction partners.     

Association of fecal microbial diversity and taxonomy with selected enzymatic functions

Few microbial functions have been compared to a comprehensive survey of the human fecal microbiome. We evaluated determinants of fecal microbial β-glucuronidase and β-glucosidase activities, focusing especially on associations with microbial alpha and beta diversity and taxonomy. We enrolled 51 healthy volunteers (26 female, mean age 39) who provided questionnaire data and multiple aliquots of a stool, from which proteins were extracted to quantify β-glucuronidase and β-glucosidase activities, and DNA was extracted to amplify and pyrosequence 16S rRNA gene sequences to classify and quantify microbiome diversity and taxonomy. Fecal β-glucuronidase was elevated with weight loss of at least 5 lb. (P = 0.03), whereas β-glucosidase was marginally reduced in the four vegetarians (P = 0.06). Both enzymes were correlated directly with microbiome richness and alpha diversity measures, directly with the abundance of four Firmicutes Clostridia genera, and inversely with the abundance of two other genera (Firmicutes Lactobacillales Streptococcus and Bacteroidetes Rikenellaceae Alistipes) (all P = 0.05-0.0001). Beta diversity reflected the taxonomic associations. These observations suggest that these enzymatic functions are performed by particular taxa and that diversity indices may serve as surrogates of bacterial functions. Independent validation and deeper understanding of these associations are needed, particularly to characterize functions and pathways that may be amenable to manipulation.     

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.     

The use of dwell time cross-correlation functions to study single-ion channel gating kinetics.

The derivation of cross-correlation functions from single-channel dwell (open and closed) times is described. Simulation of single-channel data for simple gating models, alongside theoretical treatment, is used to demonstrate the relationship of cross-correlation functions to underlying gating mechanisms. It is shown that time irreversibility of gating kinetics may be revealed in cross-correlation functions. Application of cross-correlation function analysis to data derived from the locust muscle glutamate receptor-channel provides evidence for multiple gateway states and time reversibility of gating. A model for the gating of this channel is used to show the effect of omission of brief channel events on cross-correlation functions.