Prediction and analysis of protein palmitoylation sites.

Palmitoylation is a universal and important lipid modification, involving a series of basic cellular processes, such as membrane trafficking, protein stability and protein aggregation. With the avalanche of new protein sequences generated in the post genomic era, it is highly desirable to develop computational methods for rapidly and effectively identifying the potential palmitoylation sites of uncharacterized proteins so as to timely provide useful information for revealing the mechanism of protein palmitoylation. By using the Incremental Feature Selection approach based on amino acid factors, conservation, disorder feature, and specific features of palmitoylation site, a new predictor named IFS-Palm was developed in this regard.

Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics.

Summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps.

A new test for detecting recent positive selection that is free from the confounding impacts of demography.

It has been a long-standing interest in evolutionary biology to search for the traces of recent positive Darwinian selection in organisms. However, such efforts have been severely hindered by the confounding signatures of demography. As a consequence, neutrality tests often lead to false inference of positive selection because they detect the deviation from the standard neutral model.

Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition.

Background: Metabolic pathway is a highly regulated network consisting of many metabolic reactions involving substrates, enzymes, and products, where substrates can be transformed into products with particular catalytic enzymes. Since experimental determination of the network of substrate-enzyme-product triad (whether the substrate can be transformed into the product with a given enzyme) is both time-consuming and expensive, it would be very useful to develop a computational approach for predicting the network of substrate-enzyme-product triads.

Results: A mathematical model for predicting the network of substrate-enzyme-product triads was developed.

CD81 inhibits the proliferation of astrocytes by inducing G(0)/G (1) arrest in vitro.

Astrocytes play a major role in the reactive processes in response to neuronal injuries in the brain. Excessive gliosis is detrimental and can contribute to neuronal damage. CD81 (TAPA), a member of the tetraspanin family of proteins, is upregulated by astrocytes after traumatic injury to the rat central nervous system (CNS).

Study on the enhanced fluorescent spectrum of ciprofloxacin+Al(III)+La(III)+cetyltrimethylammonium bromide system and its application.

The fluorescence of ciprofloxacin (CIP) in HAc-NaAc buffer solution and the presence of cetyltrimethylammonium bromide (CTMAB) enhanced visibly with adding Al(III) and La(III). This enhanced fluorescence spectra were studied, and a new co-luminescence system of CIP+Al(III)+La(III)+CTMAB was discovered. There was a linear relationship between the enhanced fluorescence intensity and the concentration of CIP in the range of 0.

Predicting miRNA's target from primary structure by the nearest neighbor algorithm.

We used a machine learning method, the nearest neighbor algorithm (NNA), to learn the relationship between miRNAs and their target proteins, generating a predictor which can then judge whether a new miRNA-target pair is true or not. We acquired 198 positive (true) miRNA-target pairs from Tarbase and the literature, and generated 4,888 negative (false) pairs through random combination. A 0/1 system and the frequencies of single nucleotides and di-nucleotides were used to encode miRNAs into vectors while various physicochemical parameters were used to encode the targets.

[Advances in detecting positive selection on genome].

After Darwin's natural selection theory emerged, Kimura proposed the theory of neutral evolution in 1968, which considered neutral mutations and random genetic drift as the major evolutionary forces. In the following years, various kinds of methods were developed to test whether natural selection has ever happened. With the improvement of DNA sequencing technologies, large amount of DNA sequence polymorphism data is available, providing a mass of materials for testing the natural selection theory.

A knowledge-based method to predict the cooperative relationship between transcription factors.

Identifying the cooperation between transcription factors is crucial and challenging to uncover the mystery behind the complex gene expression patterns. Computational methods aimed to infer transcription factor cooperation are expected to get good results if we can integrate the knowledge (existed functional/structural annotations) of proteins. In this contribution, we proposed an information integrative computational framework to infer the cooperation between transcription factors, which relies on the hybridization-space method that can integrate the annotation information of proteins.

Genetic optimization of photonic crystal waveguide termination for both on-axis and off-axis highly efficient directional emission.

In this work, we use the finite-difference time-domain method in conjunction with a genetic algorithm (GA) to design a photonic crystal waveguide with gratinglike surface added for highly-efficient directional emission. By placing a detector at different locations in the output field, we have obtained both on-axis and off-axis highly-efficient directional emission designs with the help of GA. The interference of light emitted from the outlet of waveguide and surfaces modes in gratinglike surface is believed to account for the directional beaming effect in our designs.

Protein sumoylation sites prediction based on two-stage feature selection.

Protein sumoylation is one of the most important post-translational modifications. Accurate prediction of sumoylation sites is very useful for the analysis of proteome. Though the putative motif Psi K XE can be used, optimization of prediction models still remains a challenge.

Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China.

The 4-bp deletion (-CTTT) at codon 41/42 (CD41/42) of the human beta-globin gene represents one of the most common beta-thalassemia mutations in East Asia and Southeast Asia, which is historically afflicted with endemic malaria, thus hypothetically evolving under natural selection by malaria infection. To understand the evolutionary process of generating the beta(CD41/42) allele and its maintenance, including the effect of natural selection on the pattern of linkage disequilibrium (LD), we sequenced a 15.933-kb region spanning 20.

Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data.

It has been hypothesized that the ratio of X-linked to autosomal sequence diversity is influenced by unequal sex ratios in Drosophila melanogaster populations. We conducted a genome scan of single nucleotide polymorphism (SNP) of 378 autosomal loci in a derived European population and of a subset of 53 loci in an ancestral African population. On the basis of these data and our already available X-linked data, we used a coalescent-based maximum-likelihood method to estimate sex ratios and demographic histories simultaneously for both populations.

[The value of arthroscopic minimally invasive surgery in diagnosis and treatment of benign bone and joint tumors].

Objective: To approach the values of arthroscopic minimally invasive surgery (MIS) in diagnosis and treatment of benign bone and joint tumors.

Method: 20 cases of benign bone and joint tumors were diagnosed and treated by arthroscopic MIS. There were 9 males and 11 females in the group.

[Spectroscopic study on the binding of Mn(II) to EHPG].

Under the conditions of 0.05 mol x L(-1) Hepes buffer at room temperature and pH 7.4, the interaction of ethylene-N,N'-bis(o-hydroxyphenylglycine) (EHPG) and Mn(II) was investigated by both fluorescence and UV difference spectra.

Inferring the demographic history and rate of adaptive substitution in Drosophila.

An important goal of population genetics is to determine the forces that have shaped the pattern of genetic variation in natural populations. We developed a maximum likelihood method that allows us to infer demographic changes and detect recent positive selection (selective sweeps) in populations of varying size from DNA polymorphism data. Applying this approach to single nucleotide polymorphism data at more than 250 noncoding loci on the X chromosome of Drosophila melanogaster from an (ancestral) African population and a (derived) European, we found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck.

Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome.

Two maximum-likelihood methods are proposed for detecting recent, strongly positive selection and for localizing the target of selection along a recombining chromosome. The methods utilize the compact mutation frequency spectrum at multiple neutral loci that are partially linked to the selected site. Using simulated data, we show that the power of the tests lies between 80 and 98% in most cases, and the false positive rate could be as low as approximately 10% when the number of sampled marker loci is sufficiently large (> or = 20).

Moderate mutation rate in the SARS coronavirus genome and its implications.

Background: The outbreak of severe acute respiratory syndrome (SARS) caused a severe global epidemic in 2003 which led to hundreds of deaths and many thousands of hospitalizations. The virus causing SARS was identified as a novel coronavirus (SARS-CoV) and multiple genomic sequences have been revealed since mid-April, 2003. After a quiet summer and fall in 2003, the newly emerged SARS cases in Asia, particularly the latest cases in China, are reinforcing a wide-spread belief that the SARS epidemic would strike back.

Neutrality tests using DNA polymorphism from multiple samples.

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data.