DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log₂-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Background: Pathogenic protozoans use extracellular vesicles (EVs) for intercellular communication and host manipulation.Acanthamoeba castellaniiis a free-living protozoan that may cause severe keratitis and fatal granulomatous encephalitis. Although several secreted molecules have been shown to play crucial roles in the pathogenesis ofAcanthamoeba, the functions and components of parasite-derived EVs are far from understood.Methods: Purified EVs fromA. castellaniiwere confirmed by electron microscopy and nanoparticle tracking analysis. The functional roles of parasite-derived EVs in the cytotoxicity to and immune response of host cells were examined. The protein composition in EVs fromA. castellaniiwas identified and quantified by LC-MS/MS analysis.Results: EVs fromA. castellaniifused with rat glioma C6 cells. The parasite-derived EVs induced an immune response from human THP-1 cells and a cytotoxic effect in C6 cells. Quantitative proteomic analysis identified a total of 130 proteins in EVs. Among the identified proteins, hydrolases (50.2%) and oxidoreductases (31.7%) were the largest protein families in EVs. Furthermore, aminopeptidase activities were confirmed in EVs fromA. castellanii.Conclusions: The proteomic profiling and functional characterization of EVs fromA. castellaniiprovide an in-depth understanding of the molecules packaged into EVs and their potential mechanisms mediating the pathogenesis of this parasite.

Toxoplasma gondii is an opportunistic, zoonotic pathogen with a worldwide distribution. There are large variations in the seroprevalence of T. gondii infection in different regions of the world. Although toxoplasmosis became a notifiable communicable disease in Taiwan in 2007, little is known about its epidemiology among the general population. This cross-sectional study aimed to survey the seroprevalence of T. gondii infection and its risk factors among healthy blood donors in Taiwan. Through collaborating with the Taiwan Blood Services Foundation, a total of 1,783 healthy blood donors from all six-branch blood service centers participated in this study. The blood samples were tested for the presence of T. gondii antibodies and DNA using enzyme immunoassays and real-time PCR, respectively. Structured questionnaires were used to gather information on risk factors for T. gondii infection. Of the 1,783 participants, 166 (9.3%) tested positive for anti-Toxoplasma IgG, while 5 (0.28%) tested positive for anti-Toxoplasma IgM. The five IgM positive donors had high avidity antibodies suggestive of past infection. No active parasitemia was detected by real-time PCR assays. Multivariate logistic regression showed that undercooked pork meat consumption (adjusted odds ratio [OR] = 2.9; 95% confidence interval [CI]: 1.3–6.5), raw mussels consumption (adjusted OR = 5.3; 95% CI: 1.5–19.1), having a cat in the household (adjusted OR = 2.0; 95% CI: 1.2–3.2), a lower education level (adjusted OR = 1.6; 95% CI: 1.1–2.3), and donation place in eastern Taiwan (adjusted OR = 2.5; 95% CI: 1.6–3.9) were independent risk factors for Toxoplasma seropositivity. These findings provide information on the seroprevalence and epidemiology of T. gondii infection among healthy blood donors in Taiwan.

Acanthamoeba keratitis (AK), a painful infectious corneal disease, is caused by the free-living pathogenic species Acanthamoeba. The symptoms include corneal infiltrate, epithelial, and stromal destruction, and loss of vision. Current treatment generally involves an hourly application of polyhexamethylene biguanide (PHMB) over a period of several days; however, even this is not entirely effective against all strains/isolates. The aims of this study were to confirm the existence of pathogenic strains in Taiwan which are highly resistant to drugs and to characterize the behavior of these strains. An in vitro Acanthamoeba species culture platform was established to observe the effectiveness of treatment and chart the morphological changes that occur under the effects of drugs using a light microscope and time-lapse recording. Changes in gene expression were examined using reverse transcription polymerase chain reaction (RT-PCR) and real-time PCR. Over 90% of the standard strain cells (ATCC 30010) were lysed after being treated with PHMB for 1 hour; however, clinical isolates of Acanthamoeba castellanii that differed in their susceptibility to the treatment drug were only partly lysed. Following treatment with PHMB, National Cheng Kung University Hospital isolation B (NCKH_B) transformed into a pseudocyst under the effects of drug stress; however, National Cheng Kung University Hospital isolation D (NCKH_D), an isolate with higher tolerance for PHMB, did not transform. Our results confirm the existence of clinical isolates of A. castellanii with high resistance to PHMB in Taiwan and present the alternative drug tolerance of A. castellanii in addition to the transformation of pseudocyst/cyst.