Identification and characterization of microRNAs in Clonorchis sinensis of human health significance

<p>Abstract</p> <p>Background</p> <p><it>Clonorchis sinensis </it>is a zoonotic parasite causing clonorchiasis-associated human disease such as biliary calculi, cholecystitis, liver cirrhosis, and it is currently classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules which are essential for the complex life cycles of parasites and are involved in parasitic infections. To identify and characterize miRNAs expressed in adult <it>C. sinensis </it>residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing and bioinformatic predictions with stem-loop real-time PCR analysis.</p> <p>Results</p> <p>Here we report the use of this approach to identify and clone 6 new and 62,512 conserved <it>C. sinensis </it>miRNAs which belonged to 284 families. There was strong bias on families, family members and sequence nucleotides in <it>C. sinensis</it>. Uracil was the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and end of conserved miRNAs. There was no significant "seed region" at the first and ninth positions which were commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of <it>C. sinensis </it>were still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There were two miRNA strategies in <it>C. sinensis </it>for its parasitic life: keeping a large category of miRNA families of different animals and keeping stringent conserved seed regions with high active innovation in other places of miRNAs mainly in the middle and the end, which were perfect for the parasite to perform its complex life style and for host changes.</p> <p>Conclusions</p> <p>The present study represented the first large scale characterization of <it>C. sinensis </it>miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as miRNA studies of other related species such as <it>Opisthorchis viverrini </it>and <it>Opisthorchis felineus </it>of human and animal health significance.</p

Stray dogs as indicators of Toxoplasma gondii distributed in the environment: the first report across an urban-rural gradient in China

<p>Abstract</p> <p>Background</p> <p>Toxoplasmosis is an important parasitic zoonosis caused by the protozoan <it>Toxoplasma gondii </it>that is distributed world-wide and infects a variety of hosts. However, the prevalence of <it>T. gondii </it>in the environment (such as soil, water and food) is largely unknown. Due to the technical difficulty in oocyst counting directly, an alternative assay using the serologic status of <it>T. gondii </it>in free-living animals, such as stray or free-living dogs, as an indicator, can be used to evaluate environmental contamination indirectly, as they are exposed to the same risk of infection as humans and other animals.</p> <p>Results</p> <p>In the present study, 231 stray or free-living dogs across an urban-rural gradient were examined to assess the frequency of <it>T. gondii </it>in the environment. Specific antibodies to <it>T. gondii </it>were found in 93 dogs (40.3%) by enzyme-linked immunosorbent assay (ELISA), and no statistically significant differences were observed in seroprevalences of <it>T. gondii </it>between urban dogs (38.7%) and rural dogs (41%) (<it>p </it>> 0.05).</p> <p>Conclusions</p> <p>A high seroprevalence of <it>T. gondii </it>in stray or free-living dogs in the present study indicates that there would be a wide distribution and a constant infection pressure of <it>T. gondii </it>across an urban-rural gradient, and the oocysts of <it>T. gondii </it>in the environment would be an important source of infection for humans and other animals both in urban and rural areas in China.</p

A Global Characterization and Identification of Multifunctional Enzymes

Multi-functional enzymes are enzymes that perform multiple physiological functions. Characterization and identification of multi-functional enzymes are critical for communication and cooperation between different functions and pathways within a complex cellular system or between cells. In present study, we collected literature-reported 6,799 multi-functional enzymes and systematically characterized them in structural, functional, and evolutionary aspects. It was found that four physiochemical properties, that is, charge, polarizability, hydrophobicity, and solvent accessibility, are important for characterization of multi-functional enzymes. Accordingly, a combinational model of support vector machine and random forest model was constructed, based on which 6,956 potential novel multi-functional enzymes were successfully identified from the ENZYME database. Moreover, it was observed that multi-functional enzymes are non-evenly distributed in species, and that Bacteria have relatively more multi-functional enzymes than Archaebacteria and Eukaryota. Comparative analysis indicated that the multi-functional enzymes experienced a fluctuation of gene gain and loss during the evolution from S. cerevisiae to H. sapiens. Further pathway analyses indicated that a majority of multi-functional enzymes were well preserved in catalyzing several essential cellular processes, for example, metabolisms of carbohydrates, nucleotides, and amino acids. What’s more, a database of known multi-functional enzymes and a server for novel multi-functional enzyme prediction were also constructed for free access at http://bioinf.xmu.edu.cn/databases/MFEs/index.htm

Using neural networks to forecast available system resources: an approach and empirical investigation

Software aging refers to the phenomenon that software systems show progressive performance degradation or a sudden crash after longtime execution. It has been reported that this phenomenon is closely related to the exhaustion of system resources. This paper quantitatively studies available system resources under the real-world situation where workload changes dynamically over time. We propose a neural network approach to first investigate the relationship between available system resources and system workload and then to forecast future available system resources. Experimental results on data sets collected from real-world computer systems demonstrate that the proposed approach is effective

The inflammation influence on corneal surface after frontalis suspension surgery

AIM: To study the influence of frontalis muscle flap suspension on ocular surface by analyzing the clinical features and inflammatory cytokines. METHODS: A prospective, observational case series. Thirty-one eyes of 25 patients with severe congenital blepharoptosis who underwent frontalis muscle flap suspension surgery with at least 6mo of follow-up were included in the study. The main outcome measures were margin reflex distance 1 (MRD1), degree of lagophthalmos, ocular surface disease index (OSDI), fluorescein staining (Fl), tear break-up time (BUT), Schirmer I test, and inflammatory cytokine assay. RESULTS: The degrees of lagophthalmos significantly increased after surgery. The OSDI scores significantly increased 1wk postoperatively and then decreased 4wk after operation. The Fl scores reflected corneal epithelial defects in sixteen patients at early stage postoperatively. The BUT and Schirmer I test values remained stable and did not show change compared to those before surgery. The inflammatory cytokines in conjunctival epithelial cells (including IL-1β, IL-6, IL-8, TNF-α, and IL-17A) significantly increased 1wk after the surgery (P<0.001), then returned to the normal level at 24wk postoperatively. The levels of inflammatory cytokine IL-1β, IL-6, IL-8, TNF-α, and IL-17A elevated significantly and were positively correlated with OSDI and Fl scores. CONCLUSION: Frontalis muscle flap suspension surgery results in lagophthalmos in early period of post-operation and relieved after months. The elevation of inflammatory cytokines level may participate in the occurrence of corneal epithelial defects at the early postoperative stage