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PubMed2006

Generalized Haar DWT and transformations between decision trees and neural networks.

The core contribution of this paper is a three-fold improvement of the Haar discrete wavelet transform (DWT). It is modified to efficiently transform a multiclass- (rather than numerical-) valued function over a multidimensional (rather than low dimensional) domain, or transform a multiclass-valued decision tree into another useful representation. We prove that this multidimensional, multiclass DWT uses dynamic programming to minimize (within its framework) the number of nontrivial wavelet coefficients needed to summarize a training set or decision tree. It is a spatially localized algorithm that takes linear time in the number of training samples, after a sort. Convergence of the DWT to benchmark training sets seems to degrade with rising dimension in this test of high dimensional wavelets, which have been seen as difficult to implement. This multiclass multidimensional DWT has tightly coupled applications from learning "dyadic" decision trees directly from training data, rebalancing or converting preexisting decision trees to fixed depth boolean or threshold neural networks (in effect parallelizing the evaluation of the trees), or learning rule/exception sets represented as a new form of tree called an "E-tree", which could greatly help interpretation/visualization of a dataset.

Journal Article↗

PubMed2005

Genetically optimized fuzzy decision trees.

In this study, we are concerned with genetically optimized fuzzy decision trees (G-DTs). Decision trees are fundamental architectures of machine learning, pattern recognition, and system modeling. Starting with the generic decision tree with discrete or interval-valued attributes, we develop its fuzzy set-based generalization. In this generalized structure we admit the values of the attributes that are represented by some membership functions. Such fuzzy decision trees are constructed in the setting of genetic optimization. The underlying genetic algorithm optimizes the parameters of the fuzzy sets associated with the individual nodes where they play a role of fuzzy "switches" by distributing a flow of processing completed within the tree. We discuss various forms of the fitness function that help capture the essence of the problem at hand (that could be either of classification nature when dealing with discrete outputs or regression-like when handling a continuous output variable). We quantify a nature of the generalization of the tree by studying an optimally adjusted spreads of the membership functions located at the nodes of the decision tree. A series of experiments exploiting synthetic and machine learning data is used to illustrate the performance of the G-DTs.

Algorithms↗

PubMedDate not supplied

Smashing peacocks further: drawing quasi-trees from biconnected components.

Quasi-trees, namely graphs with tree-like structure, appear in many application domains, including bioinformatics and computer networks. Our new SPF approach exploits the structure of these graphs with a two-level approach to drawing, where the graph is decomposed into a tree of biconnected components. The low-level biconnected components are drawn with a force-directed approach that uses a spanning tree skeleton as a starting point for the layout. The higher-level structure of the graph is a true tree with meta-nodes of variable size that contain each biconnected component. That tree is drawn with a new area-aware variant of a tree drawing algorithm that handles high-degree nodes gracefully, at the cost of allowing edge-node overlaps. SPF performs an order of magnitude faster than the best previous approaches, while producing drawings of commensurate or improved quality.

Journal Article↗

PubMed2004

Long-distance pollen flow and tolerance to selfing in a neotropical tree species.

Outcrossing rates, pollen dispersal and male mating success were assessed in Dicorynia guianensis Amshoff, a neotropical tree endemic to the Guiana shield. All adult trees within a continuous area of 40 ha (n = 157) were mapped, and were genotyped with six microsatellite loci. In addition, progenies were genotyped from 22 mature trees. At the population level, the species was mostly outcrossing (tm = 0.89) but there was marked variation among individuals. One tree exhibited mixed mating, confirming earlier results obtained with isozymes that D. guianensis can tolerate selfing. A Bayesian extension of the fractional paternity method was used for paternity analysis, and was compared with the neighbourhood method used widely for forest trees. Both methods indicated that pollen dispersal was only weakly related to distance between trees within the study area, and that the majority (62%) of pollen came from outside the study stand. Using maximum likelihood, male potential population size was estimated to be 1119, corresponding to a neighbourhood size of 560 hectares. Male mating success was, however, related to the diameter of the stem and to flowering intensity assessed visually. The mating behaviour of D. guianensis is a combination of long-distance pollen flow and occasional selfing. The species can still reproduce when it is extremely rare, either by selfing or by dispersing pollen at long distances. These results, together with the observation that male mating success was correlated with the size of the trees, could be implemented in management procedures aiming at regenerating the species.

Bayes Theorem↗

PubMed2005

Scaling laws of vascular trees: of form and function.

The branching pattern and vascular geometry of biological tree structure are complex. Here we show that the design of all vascular trees for which there exist morphometric data in the literature (e.g., coronary, pulmonary; vessels of various skeletal muscles, mesentery, omentum, and conjunctiva) obeys a set of scaling laws that are based on the hypothesis that the cost of construction of the tree structure and operation of fluid conduction is minimized. The laws consist of scaling relationships between 1) length and vascular volume of the tree, 2) lumen diameter and blood flow rate in each branch, and 3) diameter and length of vessel branches. The exponent of the diameter-flow rate relation is not necessarily equal to 3.0 as required by Murray's law but depends on the ratio of metabolic to viscous power dissipation of the tree of interest. The major significance of the present analysis is to show that the design of various vascular trees of different organs and species can be deduced on the basis of the minimum energy hypothesis and conservation of energy under steady-state conditions. The present study reveals the similarity of nature's scaling laws that dictate the design of various vascular trees and the underlying physical and physiological principles.

Animals↗

PubMed1994

Impact of parallel heterogeneity on a continuum model of the pulmonary arterial tree.

Model arterial trees were constructed following rules consistent with morphometric data, Nj = (Dj/Da)-beta 1 and Lj = La(Dj/Da)beta 2, where Nj, Dj, and Lj are number, diameter, and length, respectively, of vessels in the jth level; Da and La are diameter and length, respectively, of the inlet artery, and -beta 1 and beta 2 are power law slopes relating vessel number and length, respectively, to vessel diameter. Simulated heterogeneous trees approximating these rules were constructed by assigning vessel diameters Dm = Da[2/(m + 1)]1/beta 1, such that m-1 vessels were larger than Dm (vessel length proportional to diameter). Vessels were connected, forming random bifurcating trees. Longitudinal intravascular pressure [P(Qcum)] with respect to cumulative vascular volume [Qcum] was computed for Poiseuille flow. Strahler-ordered tree morphometry yielded estimates of La, Da, beta 1, beta 2, and mean number ratio (B); B is defined by Nk + 1 = Bk, where k is total number of Strahler orders minus Strahler order number. The parameters were used in P(Qcum) = Pa [formula: see text] and the resulting P(Qcum) relationship was compared with that of the simulated tree, where Pa is total arterial pressure drop, Q is flow rate, Ra = (128 microLa)/(pi D4a (where mu is blood viscosity), and Qa (volume of inlet artery) = 1/4D2a pi La. Results indicate that the equation, originally developed for homogeneous trees (J. Appl. Physiol. 72: 2225-2237, 1992), provides a good approximation to the heterogeneous tree P(Qcum).

Algorithms↗

PubMedDate not supplied

Functional characteristics of optimized arterial tree models perfusing volumes of different thickness and shape.

The relationship between the 'shape of an organ' and the 'cost of blood transport' to perfuse its tissue was evaluated on the basis of optimized arterial model trees simulated to perfuse square-based 100-cm(3) volumes of different shape ('flat' versus 'thick' as defined by the ratio of thickness to side-length h/s < or =1). Specifically, the effects of 'shape' on tree structure, blood transport, and on hemodynamic characteristics were investigated. Branching models of arterial trees were generated by constrained constructive optimization (CCO), based on an identical set of model parameters. All model trees were geometrically and topologically optimized for intravascular volume. Tree structures achieved tremendous savings of blood (transport medium) in comparison to a system of separate tubes. Thickening the perfusion volume (increasing h/s) resulted in a significant decrease of mean transport length, deposition time, and intravascular total volume in the tree. 'Thick' perfusion volumes induced CCO trees to branch more symmetrically into a number of equivalent subtrees repetitiously splitting into smaller ones; 'flat' structures were dominated throughout by a few asymmetrically branching major vessels. In summary, we conclude from systematic variation of shape that thicker perfusion volumes (h/s >0.1) facilitate efficient delivery of blood in comparison to large amounts of 'dead volume' to be carried over long distances in very thin pieces of tissue.

Arteries↗

PubMed2001

Application of classification tree and neural network algorithms to the identification of serological liver marker profiles for the diagnosis of hepatocellular carcinoma.

OBJECTIVE: Although many attempts have been made to identify tumour-specific alpha-fetoprotein (AFP) glycoforms or other serological markers for the diagnosis of hepatocellular carcinoma (HCC), none of the available markers has, so far, shown satisfactory sensitivity and specificity. Here we aimed to apply classification tree and neural network algorithms to interpret the levels of multiple serological liver markers to improve overall specificity and sensitivity, particularly with a view to discriminating between liver cirrhosis with and without HCC. METHODS: We developed classification trees and neural networks that identified serological liver marker profiles comprising AFP, alpha1-antitrypsin (A1AT), alpha2-macroglobulin (A2MG), thyroxine-binding globulin (TBG), transferrin and albumin as well as sex and age, which might permit the diagnosis of HCC. Data were collected from 65 HCC patients, 51 patients with liver cirrhosis alone (LC) and 51 normal healthy subjects. RESULTS: The generated classification trees and neural networks showed similar diagnostic values in differentiating HCC from LC. The classification trees identified AFP, A1AT and albumin as the most important classification parameters, whereas the neural networks identified A2MG, AFP, A1AT and albumin as the predominant factors. The classification logic of the classification trees indicated that more HCC cases could be identified among cases with slightly elevated AFP levels by using the serum levels of A1AT and albumin. The neural networks were also useful for the identification of the HCC cases when the AFP levels were below 500 ng/ml (p < 0.005). The neural networks could identify HCC cases with AFP levels within the normal range, but the classification trees could not. By combining the conventional AFP test and the neural networks, the overall diagnostic sensitivity for HCC was significantly increased from 60.0 to 73.8% (p < 0.05) while maintaining a high specificity (88.2%). The sensitivities for tumors of different sizes were similar. CONCLUSION: The neural network algorithm appeared to be more powerful than the classification tree algorithm in the identification of the distinctive serological liver marker profiles for the diagnosis of the HCC subgroup without significant elevation in serum AFP levels. By incorporating serological levels of other liver markers and including data from a large number of patients and control subjects, it should prove possible to develop a versatile neural network for early diagnosis of HCC.

Adult↗

PubMed2002

Network random keys - a tree representation scheme for genetic and evolutionary algorithms.

When using genetic and evolutionary algorithms for network design, choosing a good representation scheme for the construction of the genotype is important for algorithm performance. One of the most common representation schemes for networks is the characteristic vector representation. However, with encoding trees, and using crossover and mutation, invalid individuals occur that are either under- or over-specified. When constructing the offspring or repairing the invalid individuals that do not represent a tree, it is impossible to distinguish between the importance of the links that should be used. These problems can be overcome by transferring the concept of random keys from scheduling and ordering problems to the encoding of trees. This paper investigates the performance of a simple genetic algorithm (SGA) using network random keys (NetKeys) for the one-max tree and a real-world problem. The comparison between the network random keys and the characteristic vector encoding shows that despite the effects of stealth mutation, which favors the characteristic vector representation, selectorecombinative SGAs with NetKeys have some advantages for small and easy optimization problems. With more complex problems, SGAs with network random keys significantly outperform SGAs using characteristic vectors. This paper shows that random keys can be used for the encoding of trees, and that genetic algorithms using network random keys are able to solve complex tree problems much faster than when using the characteristic vector. Users should therefore be encouraged to use network random keys for the representation of trees.

Algorithms↗

PubMed2004

Visualising very large phylogenetic trees in three dimensional hyperbolic space.

BACKGROUND: Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS: We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. CONCLUSION: Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED).

Animals↗

PubMed2005

Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.

BACKGROUND: When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies. RESULTS: We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients. CONCLUSION: A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data.

Animals↗

PubMed2006

Core set approach to reduce uncertainty of gene trees.

BACKGROUND: A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP) method frequently allows a number of topologies with a same total branching length. RESULTS: Kitazoe et al. developed multidimensional vector-space representation of phylogeny. It converts additivity of evolutionary distances to orthogonality among the vectors expressing branches, and provides a unified index to measure deviations from the orthogoality. In this paper, this index is used to detect and exclude sequences with large deviations from orthogonality, and then selects a maximum subset ("core set") of sequences for which MP generates a single solution. Once the core set tree is formed whose all the node sequences are given, the excluded sequences are found to have basically two phylogenetic positions on this tree, respectively. Fortunately, since multiple substitutions are rare in intra-species sequences, the variance of nucleotide transitions is confined to a small range. By applying the core set approach to 38 partial env sequences of HIV-1 in a single patient and also 198 mitochondrial COI and COII DNA sequences of Anopheles dirus, we demonstrate how consistently this approach constructs the tree. CONCLUSION: In the HIV dataset, we confirmed that the obtained core set tree is the unique maximum set for which MP proposes a single tree. In the mosquito data set, the fluctuation of nucleotide transitions caused by the sequences excluded from the core set was very small. We reproduced this core-set tree by simulation based on random process, and applied our approach to many sets of the obtained endpoint sequences. Consequently, the ninety percent of the endpoint sequences was identified as the core sets and the obtained node sequences were perfectly identical to the true ones.

Animals↗

PubMed1998

Comparison of three-dimensional virtual endoscopy with bronchoscopy in patients with oesophageal carcinoma infiltrating the tracheobronchial tree.

Virtual endoscopy (VE) is a technique for performing simulated bronchoscopy using helical CT data of the tracheobronchial tree. In order to evaluate a virtual three-dimensional (3D) endoluminal procedure for the tracheobronchial tree, comparison was made between bronchoscopy, axial CT images and minimal intensity projections (MIP). 21 patients were referred for helical CT because of oesophageal carcinoma shown by bronchoscopy to infiltrate into the trachea or bronchi. Axial CT images obtained on a helical scanner were transferred to a Sparc20 workstation. VE was compared with the axial CT images and the MIP concerning additional information on the location and degree of stenosis gained after 3D reconstruction of the inner surface of the tracheobronchial tree. The accuracy of this VE system was compared with bronchoscopy. Follow-up was performed in two patients to evaluate the tracheobronchial system after stent implantation. All stenoses were identified by VE with no statistically significant difference in detection of location or grading of the stenosis to real time bronchoscopy. Passage of subtotal stenosis was only possible with VE. VE is suitable for following up stent implantation. Submucosal lesions of the tracheobronchial tree could not be detected by VE. There was no statistically significant difference regarding the location of the stenoses between VE, axial CT slices, MIP and bronchoscopy. The VE showed only a statistically significant difference with regard to the degree of stenosis which was underrated on axial CT slices and MIPs. Pitfalls including mucus plugs and wall defects due to the wrong threshold value were a limitation of VE. VE is presently too time-consuming to use in every patient with an infiltrating tumour into the tracheobronchial tree. In conclusion, while VE cannot replace endoscopy of the tracheobronchial tree or the oesophagus, it is an accurate and non-invasive method for identifying endoluminal tumours, grading stenoses and visualizing the tracheobronchial tree beyond stenoses in a small number of patients who are not amenable to endoscopy.

Aged↗

PubMedDate not supplied

Copper release from chemical root-control baskets in hardwood tree production.

The City of Montreal, Canada, evaluated the environmental impact and usefulness of in-ground copper (Cu)-treated baskets in controlling root growth of hardwood trees in nursery culture. Using baskets planted with 5-yr-old Norway maple (Acer platanoides L.) trees, the amount and temporal pattern of Cu release from the basket surface into soil was determined for two copper formulations: Cu metal powder and Cu(OH)2. Release of both Cu formulations from the basket surface decreased exponentially over time, with Cu concentration at the basket surface dropping to 2% of the initial Cu applied by the end of the second field season. Total Cu content increased significantly in the soil around the baskets (from 7 to 28 mg Cu kg(-1) soil) and in the baskets (from 7 to 50-70 mg Cu kg(-1) soil) over the two years of the study. Three levels of phosphorus application (33, 66, and 100% of the regular nursery rate of 465 kg ha(-1) yr(-1)) did not affect release of Cu from the basket surface. The release of Cu metal at 28 and 105 d in the field was significantly increased by inoculation with the symbiotic arbuscular mycorrhizal fungus (AMF) Glomus intraradices Schenck & Smith; however, AMF inoculation had no affect on Cu(OH)2 release. Trees grown in Cu-treated baskets and inoculated with G. intraradices had similar colonization to non-inoculated trees, suggesting that inoculation was not very effective and that AMF inoculum was already present in the root ball of the trees at planting. After two years, copper basket-grown trees had significantly less root colonization than isolated control trees growing in the open field. This strongly suggests that conditions inside the baskets were not favorable to AMF.

Acer↗

PubMed2004

Alteration of p53 and p21 during hepatocarcinogenesis in tree shrews.

AIM: To investigate p53 mutation and p21 expression in hepatocarcinogenesis induced by hepatitis B virus (HBV) and aflatoxin B(1) (AFB(1)) in tree shrews, and to reveal the role of these genes in hepatocarcinogenesis. METHODS: Tree shrews were divided into four groups: group A, those infected with HBV and fed with AFB(1) (n = 39); group B, those infected with HBV alone (n = 28); group C, those fed with AFB(1) alone (n = 29); and group D, normal controls (n = 20). The tree shrews underwent liver biopsies once every 15 wk. Expression of p53 and p21 proteins and genes in the biopsies and tumor tissues of the experimental tree shrews was detected, respectively, by immunohistochemistry, and by Southern blotting and reverse transcription-polymerase chain reaction and sequencing. RESULTS: The incidence of hepatocellular carcinomas (HCC) was higher in group A (66.7%) than that in group B (3.57%) and C (30%). The time of HCC occurrence was also earlier in group A than that in group C (120.0+/-16.6 wk vs 153.3+/-5.8 wk, respectively, P<0.01). p53 protein was not detected by immunohistochemistry in all groups before the 75(th) wk of the experiment. At the 105(th) wk, the positive rates fo p53 were 78.6%, 60% and 71.4% in groups A, B and C, respectively, which were significantly higher than that in group D (10%) (all P<0.05). An abnormal band of p53 gene was observed in groups A and C. The mutation points of p53 gene in tree shrews with HCC were at codons 275, 78 and 13. The nucleotide sequence and amino acid sequence of tree shrew's wild-type p53 showed 91.7% and 93.4% homologies with those of human p53, respectively. The immunopositivity for p21 was found before HCC development. The incidence of HCC was significantly higher in tree shrews that were positive for p21 than those negative for p21 (80.0% vs 11.0%, P<0.001). The incidence of HCC in p21 positive animals in group A was significantly higher than those positive for p21 in group C (P<0.05). CONCLUSION: A remarkable synergistic effect on HCC development exists between HBV and AFB(1). p53 mutation promotes the development of HCC. HBV and AFB(1) may synergistically induce p53 gene mutation, and stimulate ras gene expression. ras gene is activated at the earlier stage during hepatocarcinogenesis. p21 protein may be an early marker, and the alterations of p53 may be a late event in the development of HCC.

Animals↗

PubMed2026

LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees.

MOTIVATION: Recent dynamic lineage tracing technologies use genome editing to induce heritable mutations, or edits, that accumulate across successive cell divisions. These edits are measured using single-cell sequencing or imaging, providing data to reconstruct cell lineages at single-cell resolution. Current computational approaches to infer cell lineage trees, or phylogenies, from these data perform two separate steps: (1) Identify each cell's edits (genotype) from the raw sequencing or imaging data; (2) Infer a cell lineage tree from the cell genotypes. However, genotyping cells is an inexact process and genotype errors can yield an inaccurate lineage tree. For example, using fluorescence based-imaging to measure edits results in a high fraction (≈ 25-50%) of uncertain or erroneous genotypes. RESULTS: We introduce Lineage Analysis via Maximum Likelihood with PRobabilistic Observations (LAML-Pro), an algorithm that jointly infers cell genotypes and a cell lineage tree. LAML-Pro is based on the Probabilistic Mixed-type Missing Observation (PMMO) model, which we derive to describe both the genome editing and genotype observation processes. LAML-Pro constructs lineage trees from thousands of cells in under an hour by leveraging the sparsity of transitions under the PMMO model. On simulated data, we demonstrate that LAML-Pro corrects genotype errors and infers substantially more accurate trees than existing methods which are vulnerable to genotype errors. Applied to data from two recent imaging-based lineage tracing systems, LAML-Pro reduces genotype errors by 5-fold and produces more spatially coherent lineage trees compared to existing methods. AVAILABILITY AND IMPLEMENTATION: LAML-Pro is freely available at: github.com/raphael-group/LAML-Pro.

Journal Article↗

PubMed2001

Stochastic search strategy for estimation of maximum likelihood phylogenetic trees.

The maximum likelihood (ML) method of phylogenetic tree construction is not as widely used as other tree construction methods (e.g., parsimony, neighbor-joining) because of the prohibitive amount of time required to find the ML tree when the number of sequences under consideration is large. To overcome this difficulty, we propose a stochastic search strategy for estimation of the ML tree that is based on a simulated annealing algorithm. The algorithm works by moving through tree space by way of a "local rearrangement" strategy so that topologies that improve the likelihood are always accepted, whereas those that decrease the likelihood are accepted with a probability that is related to the proportionate decrease in likelihood. Besides greatly reducing the time required to estimate the ML tree, the stochastic search strategy is less likely to become trapped in local optima than are existing algorithms for ML tree estimation. We demonstrate the success of the modified simulated annealing algorithm by comparing it with two existing algorithms (Swofford's PAUP* and Felsenstein's DNAMLK) for several theoretical and real data examples.

Algorithms↗

PubMed2003

Cloning and characterization of cholesteryl ester transfer transfer protein isolated from the tree shrew.

OBJECTIVE: To obtain the nucleotide sequence and deduced amino acid sequence of cholesteryl ester transfer protein (CETP) cDNA from the tree shrew (Tupaia glis). METHODS: The cDNA sequence of the tree shrew CETP was obtained by utilizing the technique of switching mechanism at 5' end of RNA transcript (SMART) and rapid amplification of cDNA end (RACE) from the first strand of the cDNA. The amino acid sequence of CETP was deduced from the cDNA sequence and its primary and secondary structures were predicted. RESULTS: The sequence of CETP cDNA from tree shrew (GenBank accession number AF334033) covers 1636 bp, including 178 bp at the 3' end of the untranslated region and a 1458 bp fragment in a coding region, which provides the complete sequence of mature tree shrew CETP, although not the initiator methionine. The first 24 bp encodes a partial signal peptide. The mature protein consists of 477 amino acids and is longer than the human version by one amino acid (Gly318). Comparing this amino acid sequence with those of other animals' CETPs, the identity between tree shrew and human and rabbit CETP is 88% and 82%, respectively. The protein is extremely hydrophobic as it contains many hydrophobic residues, especially at the C-terminal, consistent with its function in the transfer of neutral lipids. The amino acid residues concerning with binding and transferring neutral lipids are highly conserved. There is a deletion of an N-linked glycosylation site at Asn342 in the tree shrew CETP protein that may participate in the removal of peripheral cholesterol and cholesteryl ester by increasing its activity of transferring cholesteryl ester. CONCLUSION: The possible glycosylation in the tree shrew CETP may be involved in the molecular mechanism of its insusceptibility to atherosclerosis.

Amino Acid Sequence↗