Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium

Background Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Results Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Conclusion Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets

Transcriptome Analysis in Chicken Cecal Epithelia upon Infection by Eimeria tenella In Vivo

Coccidiosis, caused by various Eimeria species, is a major parasitic disease in chickens. However, our understanding on how chickens respond to coccidian infection is highly limited at both molecular and cellular levels. The present study employed the Affymetrix chicken genome array and performed transcriptome analysis on chicken cecal epithelia in response to infection for 4.5 days in vivo by the cecal-specific species E. tenella. By Significance Analysis of Microarrays (SAM), we have identified 7,099 probe sets with q-values at <0.05, in which 4,033 and 3,066 genes were found to be up- or down-regulated in response to parasite infection. The reliability of the microarray data were validated by real-time qRT-PCR of 20 genes with varied fold changes in expression (i.e., correlation coefficient between microarray and qRT-PCR datasets: R (2) = 0.8773, p<0.0001). Gene ontology analysis, KEGG pathway mapping and manual annotations of regulated genes indicated that up-regulated genes were mainly involved in immunity/defense, responses to various stimuli, apoptosis/cell death and differentiation, signal transduction and extracellular matrix (ECM), whereas down-regulated genes were mainly encoding general metabolic enzymes, membrane components, and some transporters. Chickens mustered complex cecal eipthelia molecular and immunological responses in response to E. tenella infection, which included pathways involved in cytokine production and interactions, natural killer cell mediated cytotoxicity, and intestinal IgA production. In response to the pathogenesis and damage caused by infection, chicken cecal epithelia reduced general metabolism, DNA replication and repair, protein degradation, and mitochondrial functions

Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica

Protection against Asiatic Taenia solium Induced by a Recombinant 45W-4B Protein▿

Taenia solium is a great threat not only to human health but also to the pig-raising industry. Oncospheral stage-specific 45W proteins are good candidates for the development of anticysticercosis vaccines. In this study, a recombinant 45W-4B protein was highly produced and used for vaccination. Two animal trials resulted in a significant reduction in parasite burden induced by the definite protein against Asiatic T. solium, up to 97.0% and 98.4%, respectively. These provide informative results for the development of effective 45W-4B vaccines against cysticercosis caused by both Chinese and Mexican T. solium isolates and even by other isolates

Comprehensive proteomic analysis of lysine acetylation in the foodborne pathogen Trichinella spiralis

Lysine acetylation is a dynamic and highly conserved post-translational modification that plays a critical role in regulating diverse cellular processes. Trichinella spiralis is a foodborne parasite with a considerable socio-economic impact. However, to date, little is known regarding the role of lysine acetylation in this parasitic nematode. In this study, we utilized a proteomic approach involving anti-acetyl lysine-based enrichment and highly sensitive mass spectrometry to identify the global acetylated proteome and investigate lysine acetylation in T. spiralis. In total, 3872 lysine modification sites were identified in 1592 proteins that are involved in a wide variety of biological processes. Consistent with the results of previous studies, a large number of the acetylated proteins appear to be involved in metabolic and biosynthetic processes. Interestingly, according to the functional enrichment analysis, 29 acetylated proteins were associated with phagocytosis, suggesting an important role of lysine acetylation in this process. Among the identified proteins, 15 putative acetylation motifs were detected. The presence of serine downstream of the lysine acetylation site was commonly observed in the regions surrounding the sites. Moreover, protein interaction network analysis revealed that various interactions are regulated by protein acetylation. These data represent the first report of the acetylome of T. spiralis and provide an important resource for further explorations of the role of lysine acetylation in this foodborne pathogen

Both unilateral and bilateral pedicle screw fixation are effective for lumbar spinal fusion—A meta-analysis-based systematic review

A series of studies have been conducted to evaluate the effectiveness of unilateral versus bilateral pedicle screw fixation in lumbar spinal fusion, but there is still controversy about which one is more superior. We performed a meta-analysis to more accurately estimate the effectiveness of unilateral versus bilateral pedicle screw fixation in lumbar spinal fusion. Studies on the comparison between unilateral and bilateral pedicle screw fixation in lumbar spinal fusion were identified from PubMed, SpringerLink, China National Knowledge Infrastructure (CNKI), the Wanfang database and the China Biology Medical literature database (CBM) and related references were searched. The included trials were screened according to the criteria of inclusion and exclusion. The quality of included trials was evaluated. Data were extracted by two reviewers independently. RevMan 5.1.1 was used for data analysis. The fixed or random effect model was selected based on the heterogeneity test among studies evaluated using the I2 statistic. A total of nine studies involving 567 patients were included in the analyses for the effectiveness of unilateral versus bilateral pedicle screw fixation in lumbar spinal fusion. Unilateral pedicle screw fixation was performed in 287 patients and bilateral pedicle screw fixation in 280 patients. The results of the meta-analysis indicated that statistically significant differences were observed between the two fixation procedures with regard to mean operation time and amount of bleeding. There were no differences in hospitalisation days, fusion rate, complication rate, and excellent and good rates. This meta-analysis suggested that both unilateral and bilateral pedicle screw fixation are effective in one or two segmental lumbar spinal fusion. In comparison with bilateral fixation, unilateral fixation can shorten the operation time, reduce the amount of bleeding, and reduce medical expenses. There were similar effects with regard to hospitalisation days, fusion rate, complication rate, and excellent and good rates

Genome-Wide Comparisons of Phylogenetic Similarities between Partial Genomic Regions and the Full-Length Genome in Hepatitis E Virus Genotyping

<div><p>Besides the complete genome, different partial genomic sequences of Hepatitis E virus (HEV) have been used in genotyping studies, making it difficult to compare the results based on them. No commonly agreed partial region for HEV genotyping has been determined. In this study, we used a statistical method to evaluate the phylogenetic performance of each partial genomic sequence from a genome wide, by comparisons of evolutionary distances between genomic regions and the full-length genomes of 101 HEV isolates to identify short genomic regions that can reproduce HEV genotype assignments based on full-length genomes. Several genomic regions, especially one genomic region at the 3′-terminal of the papain-like cysteine protease domain, were detected to have relatively high phylogenetic correlations with the full-length genome. Phylogenetic analyses confirmed the identical performances between these regions and the full-length genome in genotyping, in which the HEV isolates involved could be divided into reasonable genotypes. This analysis may be of value in developing a partial sequence-based consensus classification of HEV species.</p></div

Inorganic Salt Hydrate for Thermal Energy Storage

Using phase change materials (PCMs) for thermal energy storage has always been a hot topic within the research community due to their excellent performance on energy conservation such as energy efficiency in buildings, solar domestic hot water systems, textile industry, biomedical and food agroindustry. Several literatures have reported phase change materials concerning various aspects. Among these materials, salt hydrates are worthy of exploring due to their high-energy storage density, rational price, multiple sources and relatively good thermal conductivity. This paper reviews the present state of salt hydrates PCMs targeting classification, properties, defects, possible solutions as well as their idiographic features which are suitable for applications. In addition, new trends of future research are also indicated

Phylogenetic analysis of HEV isolates based on the three reference data sets.

<p>Neighbor-joining trees were produced by using nucleotides of complete genome (data set 1) (A), using of nucleotides concatenated first and second codon sites of ORF1/ORF2 (data set2) (B), using amino acids of concatenated protein sequences of ORF1/ORF2 (data set 3) (C). Bootstraps values (>70) and scale bars are shown.</p

Sliding-window analysis of correlations between the first two codon sites in ORF2 and those in ORF1/ORF2 (data set 2).

<p>The window sizes and plotting conditions are the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115785#pone-0115785-g001" target="_blank">Fig. 1</a>. The positions represent the site positions in the alignment of ORF2.</p