一种新的基因注释语义相似度计算方法

基因本体(GO)数据库为基因提供了统一的注释,有效地解决了不同数据库描述相同基因的不一致问题。但是,根据基因注释如何比较基因的功能相似性,这个问题仍然没有得到有效解决。本文提出一种新的基因注释语义相似度计算方法,这种方法在本质上是基于基因的生物学特性,其特点在于结点的语义相似度与结点所在集合无关,只与结点在GO图的位置有关,语义相似度可被重复利用。它既考虑了基因所映射的GO结点深度,又考虑了两GO结点之间所有路径对结点语义相似度的影响。文中以酵母菌的异亮氨酸降解代谢通路和谷氨酸合成代谢通路为实验,实验结果表明这种算法能准确地计算基因注释语义相似度。     

A new topological method to measure protein structure similarity

A method for the quantitative evaluation of structural similarity between protein pairs is developed that makes use of a Delaunay-based topological mapping. The result of the mapping is a three-dimensional array which is representative of the global structural topology and whose elements can be used to construe an integral scoring scheme. This scoring scheme was tested for its dependence on the protein length difference in a pairwise comparison, its ability to provide a reasonable means for structural similarity comparison within a family of structural neighbors of similar length, and its sensitivity to the differences in protein conformation. It is shown that such a topological evaluation of similarity is capable of providing insight into these points of interest. Protein structure comparison using the method is computationally efficient and the topological scores, although providing different information about protein similarity, correlate well with the distance root-mean-square deviation values calculated by rigid-body structural alignment.     

Correlation between gene expression and GO semantic similarity

This research analyzes some aspects of the relationship between gene expression, gene function, and gene annotation. Many recent studies are implicitly based on the assumption that gene products that are biologically and functionally related would maintain this similarity both in their expression profiles as well as in their gene ontology (GO) annotation. We analyze how accurate this assumption proves to be using real publicly available data. We also aim to validate a measure of semantic similarity for GO annotation. We use the Pearson correlation coefficient and its absolute value as a measure of similarity between expression profiles of gene products. We explore a number of semantic similarity measures (Resnik, Jiang, and Lin) and compute the similarity between gene products annotated using the GO. Finally, we compute correlation coefficients to compare gene expression similarity against GO semantic similarity. Our results suggest that the Resnik similarity measure outperforms the others and seems better suited for use in gene ontology. We also deduce that there seems to be correlation between semantic similarity in the GO annotation and gene expression for the three GO ontologies. We show that this correlation is negligible up to a certain semantic similarity value; then, for higher similarity values, the relationship trend becomes almost linear. These results can be used to augment the knowledge provided by clustering algorithms and in the development of bioinformatic tools for finding and characterizing gene products.     

A graph-based semantic similarity measure for the gene ontology

Existing methods for calculating semantic similarities between pairs of Gene Ontology (GO) terms and gene products often rely on external databases like Gene Ontology Annotation (GOA) that annotate gene products using the GO terms. This dependency leads to some limitations in real applications. Here, we present a semantic similarity algorithm (SSA), that relies exclusively on the GO. When calculating the semantic similarity between a pair of input GO terms, SSA takes into account the shortest path between them, the depth of their nearest common ancestor, and a novel similarity score calculated between the definitions of the involved GO terms. In our work, we use SSA to calculate semantic similarities between pairs of proteins by combining pairwise semantic similarities between the GO terms that annotate the involved proteins. The reliability of SSA was evaluated by comparing the resulting semantic similarities between proteins with the functional similarities between proteins derived from expert annotations or sequence similarity. Comparisons with existing state-of-the-art methods showed that SSA is highly competitive with the other methods. SSA provides a reliable measure for semantics similarity independent of external databases of functional-annotation observations.     

IntelliGO: a new vector-based semantic similarity measure including annotation origin

Background  

The Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source in bioinformatics for annotating genes and measuring their semantic similarity. These measures generally involve the GO graph structure, the information content of GO aspects, or a combination of both. However, only a few of the semantic similarity measures described so far can handle GO annotations differently according to their origin (i.e. their evidence codes).     

A new method to measure foot contact

A new method to measure foot contact is described. It consists of a pressure sensitive transducer attached to one end of a flexible silicone rubber tube. A reliable indicator of foot contact is obtained with the tube glued to the outer perimeter of the sole of a shoe.     

A new method to measure autophagy flux in the nervous system

A current need in the neuroscience field is a simple method to monitor autophagic activity in vivo in neurons. Until very recently, most reports have been based on correlative and static determinations of the expression levels of autophagy markers in the brain, generating conflicting interpretations. Autophagy is a fundamental process mediating the degradation of diverse cellular components, including organelles and protein aggregates at basal levels, whereas alterations in the process (i.e., autophagy impairment) operate as a pathological mechanism driving neurodegeneration in most prevalent diseases. We have recently described a new simple method to deliver and express an autophagy flux reporter through the peripheral and central nervous system of mice by the intracerebroventricular delivery of adeno-associated viruses (AAV) into newborn mice. We obtained a wide expression of a monomeric tandem mCherry-GFP-LC3 construct in neurons through the nervous system and demonstrated efficient and accurate measurements of LC3 flux after pharmacological stimulation of the pathway or in disease settings of axonal damage. Here we discuss the possible applications of this new method to assess autophagy activity in neurons in vivo.     

A new method to measure cortical growth in the developing brain

Folding of the cerebral cortex is a critical phase of brain development in higher mammals but the biomechanics of folding remain incompletely understood. During folding, the growth of the cortical surface is heterogeneous and anisotropic. We developed and applied a new technique to measure spatial and directional variations in surface growth from longitudinal magnetic resonance imaging (MRI) studies of a single animal or human subject. MRI provides high resolution 3D image volumes of the brain at different stages of development. Surface representations of the cerebral cortex are obtained by segmentation of these volumes. Estimation of local surface growth between two times requires establishment of a point-to-point correspondence ("registration") between surfaces measured at those times. Here we present a novel approach for the registration of two surfaces in which an energy function is minimized by solving a partial differential equation on a spherical surface. The energy function includes a strain-energy term due to distortion and an "error energy" term due to mismatch between surface features. This algorithm, implemented with the finite element method, brings surface features into approximate alignment while minimizing deformation in regions without explicit matching criteria. The method was validated by application to three simulated test cases and applied to characterize growth of the ferret cortex during folding. Cortical surfaces were created from MRI data acquired in vivo at 14 days, 21 days, and 28 days of life. Deformation gradient and Lagrangian strain tensors describe the kinematics of growth over this interval. These quantitative results illuminate the spatial, temporal, and directional patterns of growth during cortical folding.     

A new method to measure autophagy flux in the nervous system

A current need in the neuroscience field is a simple method to monitor autophagic activity in vivo in neurons. Until very recently, most reports have been based on correlative and static determinations of the expression levels of autophagy markers in the brain, generating conflicting interpretations. Autophagy is a fundamental process mediating the degradation of diverse cellular components, including organelles and protein aggregates at basal levels, whereas alterations in the process (i.e., autophagy impairment) operate as a pathological mechanism driving neurodegeneration in most prevalent diseases. We have recently described a new simple method to deliver and express an autophagy flux reporter through the peripheral and central nervous system of mice by the intracerebroventricular delivery of adeno-associated viruses (AAV) into newborn mice. We obtained a wide expression of a monomeric tandem mCherry-GFP-LC3 construct in neurons through the nervous system and demonstrated efficient and accurate measurements of LC3 flux after pharmacological stimulation of the pathway or in disease settings of axonal damage. Here we discuss the possible applications of this new method to assess autophagy activity in neurons in vivo.     

A new method to measure post-traumatic joint contractures in the rabbit knee

A new device and method to measure rabbit knee joint angles are described. The method was used to measure rabbit knee joint angles in normal specimens and in knee joints with obvious contractures. The custom-designed and manufactured gripping device has two clamps. The femoral clamp sits on a pinion gear that is driven by a rack attached to a materials testing system. A 100 N load cell in series with the rack gives force feedback. The tibial clamp is attached to a rotatory potentiometer. The system allows the knee joint multiple degrees-of-freedom (DOF). There are two independent DOF (compression-distraction and internal-external rotation) and two coupled motions (medial-lateral translation coupled with varus-valgus rotation; anterior-posterior translation coupled with flexion-extension rotation). Knee joint extension-flexion motion is measured, which is a combination of the materials testing system displacement (converted to degrees of motion) and the potentiometer values (calibrated to degrees). Internal frictional forces were determined to be at maximum 2% of measured loading. Two separate experiments were performed to evaluate rabbit knees. First, normal right and left pairs of knees from four New Zealand White (NZW) rabbits were subjected to cyclic loading. An extension torque of 0.2 Nm was applied to each knee. The average change in knee joint extension from the first to the fifth cycle was 1.9 deg +/- 1.5 deg (mean +/- sd) with a total of 49 tests of these eight knees. The maximum extension of the four left knees (tested 23 times) was 14.6 deg +/- 7.1 deg, and of the four right knees (tested 26 times) was 12.0 deg +/- 10.9 deg. There was no significant difference in the maximum extension between normal left and right knees. In the second experiment, nine skeletally mature NZW rabbits had stable fractures of the femoral condyles of the right knee that were immobilized for five, six or 10 weeks. The left knee served as an unoperated control. Loss of knee joint extension (flexion contracture) was demonstrated for the experimental knees using the new methodology where the maximum extension was 35 deg +/- 9 deg, compared to the unoperated knee maximum extension of 11 deg +/- 7 deg, 10 or 12 weeks after the immobilization was discontinued. The custom gripping device coupled to a materials testing machine will serve as a measurement test for future studies characterizing a rabbit knee model of post-traumatic joint contractures.     

A new method to measure the haemoglobin oxygen saturation by the oxygen electrode

We describe a new polarographic method to measure the haemoglobin oxygen saturation in whole blood, employing up to 10 μl of sample in a standard case. The measurement is done in an anaerobic staineless-steel cuvette (1 ml) recording three oxygen tension values: (1) that of an air-equilibrated buffer before the addition of the sample; (ii) that after the addition of the sample; and (iii) that after the addition of an oxidant. The haemoglobin oxygen saturation is then calculated from the three oxygen tension values, the volume of the reagents, and solubility coefficient of oxygen. This method is simple, inexpensive and accurate, and correlates well with other standard methods.     

A new measure for functional similarity of gene products based on Gene Ontology

Background  

Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role.     

A new method to measure nasal impedance in spontaneously breathing adults

As an alternative to standard rhinomanometric methods, we applied forced oscillations at the mouth in five normal subjects and determined their nasal impedance with a novel method involving flow subtraction. Pressure oscillations of constant amplitude were applied at the mouth of a subject both when the nostrils were open and when they were closed with a noseclip. The airflows measured under the two conditions were subtracted to yield the oscillating nasal airflow at the imposed pressure. The resultant pressure-flow relation defined the nasal impedance of the subject. For frequencies between 3 and 15 Hz, the transnasal pressure-flow relation was well described by a linear lumped parameter model consisting of a resistive and inertial element. Nasal resistance obtained with flow subtraction did not differ significantly from control measurements obtained while the subjects performed the Valsalva maneuver. In contrast, nasal inertance obtained with flow subtraction was approximately twice that obtained with the Valsalva method. The difference between inertances may reflect structural changes in nasopharyngeal dimensions that occur with the Valsalva maneuver. We conclude that the mechanical impedance of the nasal passage may be determined during spontaneous breathing from the response to imposed forced oscillations at the mouth. The noninvasive nature of this method suggests that it may be simpler to implement than traditional rhinomanometric methods.     

A new method to measure leaf age: Leaf measuring-interval index

We propose a new method, the leaf measuring-interval index (LMI), to estimate leaf age in morphological and physiological studies of leaves. When the plastochron, the interval between the initiation of successive leaves, is constant, the well-known leaf plastochron index (LPI) provides a robust measure of leaf age. When the duration of the plastochron is not uniform, however, we show that the LPI can (in simulations) and does (with actual data) turn variation in duration of the plastochron into variance about the regression estimates of leaf growth curves. The method we present in this paper, the LMI, is plastochron independent. This new method is particularly suited, therefore, for studies of plants growing in natural environments rather than in controlled growth facilities where the assumptions of the LPI method can be met.     

A new method to measure plant water uptake and transpiration simultaneously

A new weighing lysimeter system is described measuring transpirationand water uptake simultaneously on one plant, growing in waterculture. The measurements may be made for short time intervals(min) making it possible to monitor quick responses to changingenvironmental conditions. Fresh weight change, a combinationof growth and water status alterations in the plant, may becalculated from transpiration and water uptake. The system consistsof two communicating vessels filled with nutrient solution;each placed on an electronic balance. One of these vessels carriesthe plant and is connected to the other by a flexible tube.Water uptake will cause an equal decrease of the solution levelin each vessel. The weight decrease of the vessel with no plantprovides a measure of water uptake, the total weight decreaseon both balances represents transpiration. Test observations showed that measurements of transpirationand water uptake in a greenhouse can be made to an accuracyof about 0.03 g min^–1 plant^–1. With fluctuatingradiation, a clearly radiation-dependent transpiration was measuredon a tomato plant in a greenhouse. These measurements showeda delay between transpiration and water uptake. Consequently,fresh weight also fluctuated with radiation. An immediate decreasein transpiration was measured upon closure of a screen in thegreenhouse, accompanied by an increase in fresh weight. Fromlate afternoon until sunrise a constant fresh weight increasewas measured; first at a relatively high rate probably due togrowth and recovering from water deficits, thereafter at a constantrate probably only due to growth. Key words: Transpiration, water uptake, water relations, tomato, lysimeter