Protein subcellular localization prediction of eukaryotes using a knowledge-based approach

<p>Abstract</p> <p>Background</p> <p>The study of protein subcellular localization (PSL) is important for elucidating protein functions involved in various cellular processes. However, determining the localization sites of a protein through wet-lab experiments can be time-consuming and labor-intensive. Thus, computational approaches become highly desirable. Most of the PSL prediction systems are established for single-localized proteins. However, a significant number of eukaryotic proteins are known to be localized into multiple subcellular organelles. Many studies have shown that proteins may simultaneously locate or move between different cellular compartments and be involved in different biological processes with different roles.</p> <p>Results</p> <p>In this study, we propose a knowledge based method, called KnowPred_site, to predict the localization site(s) of both single-localized and multi-localized proteins. Based on the local similarity, we can identify the "related sequences" for prediction. We construct a knowledge base to record the possible sequence variations for protein sequences. When predicting the localization annotation of a query protein, we search against the knowledge base and used a scoring mechanism to determine the predicted sites. We downloaded the dataset from ngLOC, which consisted of ten distinct subcellular organelles from 1923 species, and performed ten-fold cross validation experiments to evaluate KnowPred_site's performance. The experiment results show that KnowPred_siteachieves higher prediction accuracy than ngLOC and Blast-hit method. For single-localized proteins, the overall accuracy of KnowPred_siteis 91.7%. For multi-localized proteins, the overall accuracy of KnowPred_siteis 72.1%, which is significantly higher than that of ngLOC by 12.4%. Notably, half of the proteins in the dataset that cannot find any Blast hit sequence above a specified threshold can still be correctly predicted by KnowPred_site.</p> <p>Conclusion</p> <p>KnowPred_sitedemonstrates the power of identifying related sequences in the knowledge base. The experiment results show that even though the sequence similarity is low, the local similarity is effective for prediction. Experiment results show that KnowPred_siteis a highly accurate prediction method for both single- and multi-localized proteins. It is worth-mentioning the prediction process of KnowPred_siteis transparent and biologically interpretable and it shows a set of template sequences to generate the prediction result. The KnowPred_siteprediction server is available at <url>http://bio-cluster.iis.sinica.edu.tw/kbloc/</url>.</p

Superior effects of eccentric to concentric knee extensor resistance training on physical fitness, insulin sensitivity and lipid profiles of elderly men

It has been reported that eccentric training of knee extensors is effective for improving blood insulin sensitivity and lipid profiles to a greater extent than concentric training in young women. However, it is not known whether this is also the case for elderly individuals. Thus, the present study tested the hypothesis that eccentric training of the knee extensors would improve physical function and health parameters (e.g., blood lipid profiles) of older adults better than concentric training. Healthy elderly men (60–76 years) were assigned to either eccentric training or concentric training group (n=13/group), and performed 30–60 eccentric or concentric contractions of knee extensors once a week. The intensity was progressively increased over 12 weeks from 10 to 100% of maximal concentric strength for eccentric training and from 50 to 100% for concentric training. Outcome measures were taken before and 4 days after the training period. The results showed that no sings of muscle damage were observed after any sessions. Functional physical fitness (e.g., 30-s chair stand) and maximal concentric contraction strength of the knee extensors increased greater (P ≤ 0.05) after eccentric training than concentric training. Homeostasis model assessment, oral glucose tolerance test and whole blood glycosylated hemoglobin

Contralateral versus ipsilateral protective effect against muscle damage of the elbow flexors and knee extensors induced by maximal eccentric exercise

The present study compared the ipsilateral repeated bout effect (IL-RBE) and contralateral repeated bout effect (CL-RBE) of the elbow flexors (EF) and knee flexors (KF) for the same interval between bouts to shed light on their mechanisms. Fifty-two healthy sedentary young (20–28 years) men were randomly assigned to the IL-EF, IL-KF, CL-EF, and CL-KF groups (n = 13/group). Thirty maximal eccentric contractions of the EF were performed in IL-EF and CL-EF, and 60 maximal eccentric contractions of the KF were performed in IL-KF and CL-KF, with a 2-week interval between bouts. Changes in muscle damage markers such as maximal voluntary contraction (MVC) torque, muscle soreness, and plasma creatine kinase activity, and proprioception measures before to 5 days post-exercise were compared between groups. Changes in all variables were greater (p \u3c 0.05) after the first than second bout for all groups, and the changes were greater (p \u3c 0.05) for the EF than KF. The changes in all variables after the second bout were greater (p \u3c 0.05) for the CL than IL condition for both EF and KF. The magnitude of the average protective effect was similar between CL-EF (33%) and CL-KF (32%), but slightly greater (p \u3c 0.05) for IL-EF (67%) than IL-KF (61%). These demonstrate that the magnitude of CL-RBE relative to IL-RBE was similar between the EF and KF (approximately 50%), regardless of the greater muscle damage for the EF than KF. It appears that the CL-RBE is more associated with neural adaptations at cerebrum, cerebellum, interhemispheric inhibition, and coricospinal tract, but the IL-RBE is induced by additional adaptations at muscles

Effects of unilateral eccentric versus concentric training of nonimmobilized arm during immobilization

Introduction The present study tested the hypothesis that eccentric training (ET) of nonimmobilized arm would attenuate negative effects of immobilization and provide greater protective effects against muscle damage induced by eccentric exercise after immobilization, when compared with concentric training (CT). Methods Sedentary young men were placed to ET, CT, or control group (n = 12 per group), and their nondominant arms were immobilized for 3 wk. During the immobilization period, the ET and CT groups performed five sets of six dumbbell curl eccentric-only and concentric-only contractions, respectively, at 20%-80% of maximal voluntary isometric contraction (MVCiso) strength over six sessions. MVCiso torque, root-mean square (RMS) of electromyographic activity during MVCiso, and bicep brachii muscle cross-sectional area (CSA) were measured before and after immobilization for both arms. All participants performed 30 eccentric contractions of the elbow flexors (30EC) by the immobilized arm after the cast was removed. Several indirect muscle damage markers were measured before, immediately after, and for 5 d after 30EC. Results ET increased MVCiso (17% ± 7%), RMS (24% ± 8%), and CSA (9% ± 2%) greater (P \u3c 0.05) than CT (6% ± 4%, 9% ± 4%, 3% ± 2%) for the trained arm. The control group showed decreases in MVCiso (-17% ± 2%), RMS (-26% ± 6%), and CSA (-12% ± 3%) for the immobilized arm, but these changes were attenuated greater (P \u3c 0.05) by ET (3% ± 3%, -0.1% ± 2%, 0.1% ± 0.3%) than CT (-4% ± 2%, -4% ± 2%, -1.3% ± 0.4%). Changes in all muscle damage markers after 30EC were smaller (P \u3c 0.05) for the ET and CT than the control group, and ET than the CT group (e.g., peak plasma creatine kinase activity: ET, 860 ± 688 IU L-1; CT, 2390 ± 1104 IU L-1; control, 7819 ± 4011 IU L-1). Conclusions These results showed that ET of the nonimmobilized arm was effective for eliminating the negative effects of immobilization and attenuating eccentric exercise-induced muscle damage after immobilization

Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing

Angiostrongylus cantonensis is an important zoonotic nematode. It is the causative agent of eosinophilic meningitis and eosinophilic meningoencephalitis in humans. However, information of this parasite at the genomic level is very limited. In the present study, the transcriptomic profiles of the fifth-stage larvae (L5) of A. cantonensis were investigated by next-generation sequencing (NGS). In the NGS database established from the larvae isolated from the brain of Sprague–Dawley rats, 31,487 unique genes with a mean length of 617 nucleotides were assembled. These genes were found to have a 46.08 % significant similarity to Caenorhabditis elegans by BLASTx. They were then compared with the expressed sequence tags of 18 other nematodes, and significant matches of 36.09–59.12 % were found. Among these genes, 3,338 were found to participate in 124 Kyoto Encyclopedia of Genes and Genomes pathways. These pathways included 1,514 metabolisms, 846 genetic information processing, 358 environmental information processing, 264 cellular processes, and 91 organismal systems. Analysis of 30,816 sequences with the gene ontology database indicated that their annotations included 5,656 biological processes (3,364 cellular processes, 3,061 developmental processes, and 3,191 multicellular organismal processes), 7,218 molecular functions (4,597 binding and 3,084 catalytic activities), and 4,719 cellular components (4,459 cell parts and 4,466 cells). Moreover, stress-related genes (112 heat stress and 33 oxidation stress) and genes for proteases (159) were not uncommon. This study is the first NGS-based study to set up a transcriptomic database of A. cantonensis L5. The results provide new insights into the survival, development, and host–parasite interactions of this blood-feeding nematode. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00436-013-3495-z) contains supplementary material, which is available to authorized users

Changes in plasma C1q, apelin and adropin concentrations in older adults after descending and ascending stair walking intervention

This study compared changes in plasma complement component 1q (C1q), apelin and adropin concentrations in older obese women after descending (DSW) and ascending stair walking (ASW) training (n = 15/group) performed twice a week for 12 weeks, with gradual increases in exercise time from 5 to 60 min. Fasting blood samples were collected 3 days before the first and 4 days after the last training session. The improvements in the maximal voluntary isometric contraction (MVIC) strength of the knee extensors, functional physical fitness [e.g., 30-s chair stand (CS) performance], resting systolic blood pressure (SBP), insulin sensitivity [e.g., oral glucose tolerance test (OGTT)] and blood lipid profiles [e.g., total cholesterol (TC)] were greater (p \u3c 0.05) in the DSW than ASW group. Plasma C1q decreased (− 51 ± 30%), and apelin (23 ± 15%) and adropin (127 ± 106%) increased (p ≤ .0.05) only after DSW. Significant (p ≤ 0.01) partial correlations were found between the pre- to post-DSW changes in C1q, apelin or adropin and changes in outcome measures [e.g., C1q and MVIC (r = − 0.837), apelin and SBP (r = − 0.854), and andropin and OGTT (r = − 0.729)]. These results showed that greater decreases in plasma C1q and greater increases in apelin and adropin concentrations were associated with greater improvements in outcome measures after DSW than after ASW

Label-free quantitative proteomics of CD133-positive liver cancer stem cells

Abstract Background CD133-positive liver cancer stem cells, which are characterized by their resistance to conventional chemotherapy and their tumor initiation ability at limited dilutions, have been recognized as a critical target in liver cancer therapeutics. In the current work, we developed a label-free quantitative method to investigate the proteome of CD133-positive liver cancer stem cells for the purpose of identifying unique biomarkers that can be utilized for targeting liver cancer stem cells. Label-free quantitation was performed in combination with ID-based Elution time Alignment by Linear regression Quantitation (IDEAL-Q) and MaxQuant. Results Initially, IDEAL-Q analysis revealed that 151 proteins were differentially expressed in the CD133-positive hepatoma cells when compared with CD133-negative cells. We then analyzed these 151 differentially expressed proteins by MaxQuant software and identified 10 significantly up-regulated proteins. The results were further validated by RT-PCR, western blot, flow cytometry or immunofluorescent staining which revealed that prominin-1, annexin A1, annexin A3, transgelin, creatine kinase B, vimentin, and EpCAM were indeed highly expressed in the CD133-positive hepatoma cells. Conclusions These findings confirmed that mass spectrometry-based label-free quantitative proteomics can be used to gain insights into liver cancer stem cells.http://deepblue.lib.umich.edu/bitstream/2027.42/113089/1/12953_2012_Article_407.pd

Epstein–Barr Virus DNase (BGLF5) induces genomic instability in human epithelial cells

Epstein–Barr Virus (EBV) DNase (BGLF5) is an alkaline nuclease and has been suggested to be important in the viral life cycle. However, its effect on host cells remains unknown. Serological and histopathological studies implied that EBV DNase seems to be correlated with carcinogenesis. Therefore, we investigate the effect of EBV DNase on epithelial cells. Here, we report that expression of EBV DNase induces increased formation of micronucleus, an indicator of genomic instability, in human epithelial cells. We also demonstrate, using γH2AX formation and comet assay, that EBV DNase induces DNA damage. Furthermore, using host cell reactivation assay, we find that EBV DNase expression repressed damaged DNA repair in various epithelial cells. Western blot and quantitative PCR analyses reveal that expression of repair-related genes is reduced significantly in cells expressing EBV DNase. Host shut-off mutants eliminate shut-off expression of repair genes and repress damaged DNA repair, suggesting that shut-off function of BGLF5 contributes to repression of DNA repair. In addition, EBV DNase caused chromosomal aberrations and increased the microsatellite instability (MSI) and frequency of genetic mutation in human epithelial cells. Together, we propose that EBV DNase induces genomic instability in epithelial cells, which may be through induction of DNA damage and also repression of DNA repair, subsequently increases MSI and genetic mutations, and may contribute consequently to the carcinogenesis of human epithelial cells