Genome factor and gene pleiotropy hypotheses in protein evolution

<p>Abstract</p> <p/> <p>The debate of genomic correlations between sequence conservation, protein connectivity, gene essentiality and gene expression, has generated a number of new hypotheses that are challenging the classical framework of molecular evolution. For instance, the translational selection hypothesis claims that the determination of the rate of protein evolution is the protein stability to avoid the misfolding toxicity. In this short article, we propose that gene pleiotropy, the capacity for affecting multiple phenotypes, may play a vital role in molecular evolution. We discuss several approaches to testing this hypothesis.</p> <p>Reviewers</p> <p>This article was reviewed by Dr Eugene Koonin, Dr Arcady Mushegian and Dr Claus Wilke.</p

A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs

BACKGROUND: Phylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise sequence identity between miRNA precursors alone is often inadequate for unequivocally judging the phylogenetic relationships between miRNAs. Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results. RESULTS: In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets. We tested the PBC analysis pipeline with the miRNAs from six animal species, H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans. The resulting classification was compared with the miRNA families defined in miRBase. The two classifications were largely consistent. CONCLUSION: The PBC analysis pipeline is an efficient method for classifying large numbers of heterogeneous miRNA sequences. It requires minimum human involvement and provides measurements of the reliability of the classification results

A Study of the Evolution of Human microRNAs by Their Apparent Repression Effectiveness on Target Genes

BACKGROUND: Even though the genomes of many model species have already been sequenced, our knowledge of gene regulation in evolution is still very limited. One big obstacle is that it is hard to predict the target genes of transcriptional factors accurately from sequences. In this respect, microRNAs (miRNAs) are different from transcriptional factors, as target genes of miRNAs can be readily predicted from sequences. This feature of miRNAs offers an unprecedented vantage point for evolutionary analysis of gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we analyzed a particular aspect of miRNA evolution, the differences in the "apparent repression effectiveness (ARE)" between human miRNAs of different conservational levels. ARE is a measure we designed to evaluate the repression effect of miRNAs on target genes based on publicly available gene expression data in normal tissues and miRNA targeting and expression data. We found that ARE values of more conserved miRNAs are significantly higher than those of less conserved miRNAs in general. We also found the gain in expression abundance and broadness of miRNAs in evolution contributed to the gain in ARE. CONCLUSIONS/SIGNIFICANCE: The ARE measure quantifies the repressive effects of miRNAs and enables us to study the influences of many factors on miRNA-mediated repression, such as conservational levels and expression levels of miRNAs. The gain in ARE can be explained by the existence of a trend of miRNAs in evolution to effectively control more target genes, which is beneficial to the miRNAs but not necessarily to the organism at all times. Our results from miRNAs gave us an insight of the complex interplay between regulators and target genes in evolution

A Novel Method for the Fault Diagnosis of a Planetary Gearbox based on Residual Sidebands from Modulation Signal Bispectrum Analysis

This paper presents a novel method for the fault diagnosis of planetary gearboxes based on an accurate estimation of residual sidebands using a modulation signal bispectrum (MSB). The residual sideband resulting from the out-phase superposition of vibration waves from asymmetrical multiple meshing sources are much less influenced by gear errors than that of the in-phase sidebands. Therefore, with the accurate estimation by MSB they can produce accurate and consistent diagnosis, which are evaluated by both simulating and experimental studies. However, the commonly used in-phase sidebands have high amplitudes but include gear error effects, consequently leading to poor diagnostic results

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica

BACKGROUND: Myb proteins contain a conserved DNA-binding domain composed of one to four repeat motifs (referred to as R0R1R2R3); each repeat is approximately 50 amino acids in length, with regularly spaced tryptophan residues. Although the Myb proteins comprise one of the largest families of transcription factors in plants, little is known about the functions of most Myb genes. Here we use computational techniques to classify Myb genes on the basis of sequence similarity and gene structure, and to identify possible functional relationships among subgroups of Myb genes from Arabidopsis and rice (Oryza sativa L. ssp. indica). RESULTS: This study analyzed 130 Myb genes from Arabidopsis and 85 from rice. The collected Myb proteins were clustered into subgroups based on sequence similarity and phylogeny. Interestingly, the exon-intron structure differed between subgroups, but was conserved in the same subgroup. Moreover, the Myb domains contained a significant excess of phase 1 and 2 introns, as well as an excess of nonsymmetric exons. Conserved motifs were detected in carboxy-terminal coding regions of Myb genes within subgroups. In contrast, no common regulatory motifs were identified in the noncoding regions. Additionally, some Myb genes with similar functions were clustered in the same subgroups. CONCLUSIONS: The distribution of introns in the phylogenetic tree suggests that Myb domains originally were compact in size; introns were inserted and the splicing sites conserved during evolution. Conserved motifs identified in the carboxy-terminal regions are specific for Myb genes, and the identified Myb gene subgroups may reflect functional conservation

Modelling and Validation of a Regenerative Shock Absorber System

Abstract— For effective energy regeneration and vibration dampening, energy regenerative suspension systems have received more studies recently. This paper presents the dynamic modeling and a test system of a regenerative shock absorber system which converts vibration motion into rotary motion through the adjustment of hydraulic flow. Hydraulic circuit configuration achieves the one way flow and energy regeneration during both compression and extension strokes. The dynamic modeling is performed for the evaluation of design concept and the feasibility studies of regenerative shock absorber system theoretically. Based on simulated results, the efficiency of hydraulic transmission is optimized and validated in test system. The results show that the performance of hydraulic fluid, the features of rotary motion and the capability of energy regeneration are verified and compared between dynamic modeling and experiments. Meanwhile, the average power of 118.2W and 201.7W with the total energy conversion of 26.86% and 18.49% can be obtained based on experiments under sinusoidal inputs with 0.07854m/s and 0.1256m/s respectively

A Novel Privacy Preserving Search Technique for Stego Data in Untrusted Cloud

We propose the first privacy preserving search technique for stego health data in untrusted cloud in this paper. The Cloud computing is a popular technology to the healthcare providers for outsourcing health data due to flexibility and cost effectiveness. However, outsourcing health data to the cloud introduces serious privacy issues to the patient. For example, dishonest personnel of the cloud provider may disclose patient sensitive information to business organizations for some financial benefits. Using steganography, patient sensitive information is hidden within health data for privacy preservation. As a result, stego health data is generated. To the best of our knowledge, no method exists for searching a particular stego data without disclosing any information to the cloud. We propose a framework for privacy preserving search over stego health data. We systematically describe each component of the proposed framework. We conduct several experiments to evaluate the performance of the framework

Fast Monte Carlo Simulation for Patient-specific CT/CBCT Imaging Dose Calculation

Recently, X-ray imaging dose from computed tomography (CT) or cone beam CT (CBCT) scans has become a serious concern. Patient-specific imaging dose calculation has been proposed for the purpose of dose management. While Monte Carlo (MC) dose calculation can be quite accurate for this purpose, it suffers from low computational efficiency. In response to this problem, we have successfully developed a MC dose calculation package, gCTD, on GPU architecture under the NVIDIA CUDA platform for fast and accurate estimation of the x-ray imaging dose received by a patient during a CT or CBCT scan. Techniques have been developed particularly for the GPU architecture to achieve high computational efficiency. Dose calculations using CBCT scanning geometry in a homogeneous water phantom and a heterogeneous Zubal head phantom have shown good agreement between gCTD and EGSnrc, indicating the accuracy of our code. In terms of improved efficiency, it is found that gCTD attains a speed-up of ~400 times in the homogeneous water phantom and ~76.6 times in the Zubal phantom compared to EGSnrc. As for absolute computation time, imaging dose calculation for the Zubal phantom can be accomplished in ~17 sec with the average relative standard deviation of 0.4%. Though our gCTD code has been developed and tested in the context of CBCT scans, with simple modification of geometry it can be used for assessing imaging dose in CT scans as well.Comment: 18 pages, 7 figures, and 1 tabl