CD4+ Th immunogenicity of the Ascaris spp. secreted products

Ascaris spp. is a major health problem of humans and animals alike, and understanding the immunogenicity of its antigens is required for developing urgently needed vaccines. The parasite-secreted products represent the most relevant, yet complex (>250 proteins) antigens of Ascaris spp. as defining the pathogen-host interplay. We applied an in vitro antigen processing system coupled to quantitative proteomics to identify potential CD4+ Th cell epitopes in Ascaris-secreted products. This approach considerably restricts the theoretical list of epitopes using conventional CD4+ Th cell epitope prediction tools. We demonstrate the specificity and utility of our approach on two sets of candidate lists, allowing us identifying hits excluded by either one or both computational methods. More importantly, one of the candidates identified experimentally, clearly demonstrates the presence of pathogen-reactive T cells in healthy human individuals against these antigens. Thus, our work pipeline identifies the first human T cell epitope against Ascaris spp. and represents an easily adaptable platform for characterization of complex antigens, in particular for those pathogens that are not easily amenable for in vivo experimental validation

Reciprocal Interactions between Nematodes and Their Microbial Environments

Parasitic nematode infections are widespread in nature, affecting humans as well as wild, companion, and livestock animals. Most parasitic nematodes inhabit the intestines of their hosts living in close contact with the intestinal microbiota. Many species also have tissue migratory life stages in the absence of severe systemic inflammation of the host. Despite the close coexistence of helminths with numerous microbes, little is known concerning these interactions. While the environmental niche is considerably different, the free-living nematode Caenorhabditis elegans (C. elegans) is also found amongst a diverse microbiota, albeit on decaying organic matter. As a very well characterized model organism that has been intensively studied for several decades, C. elegans interactions with bacteria are much more deeply understood than those of their parasitic counterparts. The enormous breadth of understanding achieved by the C. elegans research community continues to inform many aspects of nematode parasitology. Here, we summarize what is known regarding parasitic nematode-bacterial interactions while comparing and contrasting this with information from work in C. elegans. This review highlights findings concerning responses to bacterial stimuli, antimicrobial peptides, and the reciprocal influences between nematodes and their environmental bacteria. Furthermore, the microbiota of nematodes as well as alterations in the intestinal microbiota of mammalian hosts by helminth infections are discussed

Using metallic photonic crystals as visible light sources

In this paper we study numerically and experimentally the possibility of using metallic photonic crystals (PCs) of different geometries (log-piles, direct and inverse opals) as visible light sources. It is found that by tuning geometrical parameters of a direct opal PC one can achieve substantial reduction of the emissivity in the infrared along with its increase in the visible. We take into account disorder of the PC elements in their sizes and positions, and get quantitative agreement between the numerical and experimental results. We analyze the influence of known temperature-resistant refractory host materials necessary for fixing the PC elements, and find that PC effects become completely destroyed at high temperatures due to the host absorption. Therefore, creating PC-based visible light sources requires that low-absorbing refractory materials for embedding medium be found.Comment: 9 pages, 15 figure

T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification

Shared and unique common genetic determinants between pediatric and adult celiac disease

Table S1. Functional profiles of the top non-HLA association signals identified in Paediatric CD and Adult CD among north Indians. Table S2. Test of heterogeneity (Breslow-Day test) for associated SNPs in PaediatricCD and AdultCD groups. Table S3. cis-eQTL evaluation of associated SNPs. Table S4. GRAIL analysis revealed seven genes with significant (p <0.05) interaction with 39 known non-HLA coeliac disease loci. These seven genes are from four loci identified in this study. (DOCX 26 kb

The Intestinal Roundworm Ascaris suum Releases Antimicrobial Factors Which Interfere With Bacterial Growth and Biofilm Formation

Ascariasis is a widespread soil-transmitted helminth infection caused by the intestinal roundworm Ascaris lumbricoides in humans, and the closely related Ascaris suum in pigs. Progress has been made in understanding interactions between helminths and host immune cells, but less is known concerning the interactions of parasitic nematodes and the host microbiota. As the host microbiota represents the direct environment for intestinal helminths and thus a considerable challenge, we studied nematode products, including excretory-secretory products (ESP) and body fluid (BF), of A. suum to determine their antimicrobial activities. Antimicrobial activities against gram-positive and gram-negative bacterial strains were assessed by the radial diffusion assay, while effects on biofilm formation were assessed using the crystal violet static biofilm and macrocolony assays. In addition, bacterial neutralizing activity was studied by an agglutination assay. ESP from different A. suum life stages (in vitro-hatched L3, lung-stage L3, L4, and adult) as well as BF from adult males were analyzed by mass spectrometry. Several proteins and peptides with known and predicted roles in nematode immune defense were detected in ESP and BF samples, including members of A. suum antibacterial factors (ASABF) and cecropin antimicrobial peptide families, glycosyl hydrolase enzymes such as lysozyme, as well as c-type lectin domain-containing proteins. Native, unconcentrated nematode products from intestine-dwelling L4-stage larvae and adults displayed broad-spectrum antibacterial activity. Additionally, adult A. suum ESP interfered with biofilm formation by Escherichia coli, and caused bacterial agglutination. These results indicate that A. suum uses a variety of factors with broad-spectrum antibacterial activity to affirm itself within its microbe-rich environment in the gut

Biowaiver monographs for immediate release solid oral dosage forms: prednisolone.

Literature data relevant to the decision to allow a waiver of in vivo bioequivalence (BE) testing for the approval of immediate release (IR) solid oral dosage forms containing prednisolone are reviewed. Data on its solubility, oral absorption, and permeability are not totally conclusive, but strongly suggest a BCS Class 1 classification. Prednisolone's therapeutic indications and therapeutic index, pharmacokinetics, and the possibility of excipient interactions were also taken into consideration. Available evidence indicates that a biowaiver for IR solid oral dosage forms formulated with the excipients tabulated in this article would be unlikely to expose patients to undue risks

Mental workload as personal data: designing a cognitive activity tracker

Research continues to correlate physical signals with mental activity, as opposed to physical activity, with physiological sensors. Further, with the proliferation of wearable technology, it seems imminent that our smart watches can soon keep track of our mental activity as well as our physical activity. Our research is working towards accurately measuring Mental Workload ‘in the wild’ using physiological sensors. While we work towards that goal, however, we have begun to explore the design aspects of representing personal cognitive data to users; analogous to a step counter for physical activity. We present the results of diary studies, focus groups, and prototyping exercises to identify design considerations for future cognitive activity trackers

Batch-fabrication of novel nanoprobes for SPM

A micromachining method has been developed for fabricating 20µm tall silicon atomic force tips with flat tops less than 2µm wide suitable for defining nanosensors upon, and with low aspect ratio sides suitable for defining electrical connections to the sensor. Methods have been developed to allow flat substrate processing techniques to be applied to such non-planar micromachined substrates. This has necessitated the development of a novel resist-coating technique and the use of defocused electron-beam lithography. Methods for through-wafer alignment by electron-beam lithography and accurate alignment to the tips using micromachined alignment markers have also had to be developed. The fabrication process has been designed to enable a wide variety of sub-micron sensors to be defined on the atomic force probes, with little additional development beyond that of : sensors themselves. This flexibility has enabled very different sensors meant for very different scanning probe microscopy techniques to be designed without significant redevelopment of the underlying fabrication process. The main restrictions on the type of sensor that can be used are the physical dimensions of the sensor, the number of alignment levels necessary, the degree of alignment accuracy required and the choice of sensor materials. However, within these constraints it has been found that probes optimised for scanning near-field optical microscopy (SNOM), scanning thermal microscopy, modulation differential scanning calorimetry (MDSC) and scanning Hall-probe microscopy can be fabricated. For the SNOM probes three methods for fabricating sub-l00nm diameter apertures have been developed, analysed and compared with each other to evaluate both the process latitude. and, the size and reproducibility of apertures that can be fabricated, as a function of electron beam dose, pattern shape and size, and metallisation material and thickness. Two methods, both utilising multilayer 'resist' schemes have been found suitable for this purpose, one based on conventional electron-beam lithography with PMMA and a new dry etching process for titanium, and the other based on a novel electron-beam lithography technique utilising cross-linked PMMA for lifting off nichrome. A simple analytical model has also been developed for these probes allowing the effects of changes in the sensor design parameters on the light throughput to be compared qualitatively, if not quantitatively. For the scanning thermal probes a method for lifting-off sub-l00nm, thin-film thermocouple sensors on silicon tips without the loss of electrical continuity has been developed. For the MDSC probes, a similar method has been developed for defining thermal resistors. A method has also been presented for fabricating sensors for scanning Hall-probe microscopy based on an evaporated germanium sensing layer. This has been found to require annealing and optimisation of sensor design and geometry to reduce sensor resistance to acceptable levels

Search, Structure, and Sentiment: A Comparative Analysis of Network Opinion in Different Query Types on Twitter

Understanding the relationship between structure and sentiment is essential in highlighting future operations with online social networks. More specifically, within popular conversation on Twitter. This paper provides a development on the relationship between the two variables: structure, defined as the composition of a directed network, and sentiment, a quantified value of the positive/negative connotations of a conversation. We highlight thread sentiment to be inversely proportional to the strength and connectivity of a network. The second portion of this paper highlights differences in query types, specifically how the aforementioned behavior differs within four key query types. This paper focuses on topical, event-based, geographic, and individual queries as orientations which have differing behavior. Using cross-query analysis, we see that the relationship between structure and sentiment, though still inversely proportional, differs greatly across query types. We find this relationship to be the most clear within the individual queries and the least prevalent within the event-based queries. This paper provides a sociological progression in our understanding of opinion and networks, while providing a methodological advancement for future studies on similar subjects