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[
J R Soc Interface,
2010]
Bio-electrospray, the direct jet-based cell handling approach, is able to handle a wide range of cells (spanning immortalized, primary to stem cells). Studies at the genomic, genetic and the physiological levels have shown that, post-treatment, cellular integrity is unperturbed and a high percentage (more than 70%, compared with control) of cells remain viable. Although, these results are impressive, it may be argued that cell-based systems are oversimplistic. Therefore, it is important to evaluate the bio-electrospray technology using sensitive and dynamically developing multi-cellular organisms that share, at least some, similarities with multi-cell microenvironments encountered with tissues and organs. This study addressed this issue by using a well-characterized model organism, the non-parasitic nematode Caenorhabditis elegans. Nematode cultures were subjected to bio-electrospraying and compared with positive (heat shock) and negative controls (appropriate laboratory culture controls). Overall, bio-electrospraying did not modulate the reproductive output or induce significant changes in in vivo stress-responsive biomarkers (heat shock proteins). Likewise, whole-genome transcriptomics could not identify any biological processes, cellular components or molecular functions (gene ontology terms) that were significantly enriched in response to bio-electrospraying. This demonstrates that bio-electrosprays can be safely applied directly to nematodes and underlines its potential future use in the creation of multi-cellular environments within clinical applications.
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[
Environ Toxicol,
2014]
Bio-oils, which are multicomponent mixtures, were produced from two different biomass (rice straw (rice oil) and sawdust of oak tree (oak oil)) by using the slow pyrolysis process, and chemical compositional screening with GC-MS detected several hazardous compounds in both bio-oil samples. The two bio-oils vary in their chemical compositional nature and concentrations. To know the actual hazard potentialities of these bio-oils, toxicological assessments were carried out in a comparative approach by using in vitro (Jurkat T and HepG2 cell) as well as in vivo (Caenorhabditis elegans) systems. A dose-dependent increase in cytotoxicity, cell death (apoptosis), and genotoxicity were observed in cultured cell systems. Similarly, the in vivo system, C. elegans also displayed a dose-dependent decrease in survival. It was found that in comparison with rice oil, oak oil displayed higher toxicity to all models systems, and the susceptibility order of the model systems were Jurkat T > HepG2 > C. elegans. Pursuing the study further toward the underlying mechanism by exploiting the C. elegans mutants screening assay, the bio-oils seem to mediate toxicity through oxidative stress and impairment of immunity. Taken together, bio-oils compositions mainly depend on the feedstock used and the pyrolysis conditions which in turn modulate their toxic potentiality.
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Probst R, Dai Q, Huang SY, Potarazu D, Christensen R, Morgan NY, Pommier Y, Xu S, Giniger E, Han X, Albrecht DR, Vishwasrao HD, Sun Y, O'Neill KM, Shroff H, Su Y, Moyle MW, White H
[
Lab Chip,
2021]
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
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[
Methods,
2016]
With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses.
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[
Sci Rep,
2017]
The discharge of engineered nanomaterials (ENMs) into environment is raising widespread concern not only due to their direction bio-toxicity but also their bio-concentration and bio-magnification through food web. However, the transformation and distribution of ENMs during food-chain transport are poorly understood, due to lack of accurate, reliable analytical methods. In this study, by using a suite of advanced spectrum techniques, we successfully tracked the distribution and biotransformation dynamics of CdSe quantum dots (QDs) during their transport from Shewanella onedensis to Caenorchabditis elegans in predation. Fluorescence microscopy and Raman mapping showed that the ingested QDs by C. elegans were located at the gut lumen and subcutaneous tissue, and were partially excreted from the nematode body over time. Micro-X-ray fluorescence (-XRF) spectroscopy and Se K-edge X-ray absorption fine structure (XAFS) results further revealed the changed distribution of Se element over time, and a shift in the major Se species from CdSe to Se(0) and Na2SeO3(IV). This work demonstrates the utility of advanced spectral techniques for characterizing QDs in vivo, and may facilitate a better understanding on the environmental transformation and fates of ENMs.
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[
Biomed Chromatogr,
2005]
An improved method for proteomics studies, which includes the fl uorogenic derivertization of protein mixtures with 7-chloro-4-(dimethylaminoethylaminosulfonyl)-2,1,3-benzoxadiazole (DAABD-Cl), followed by HPLC isolation, enzymatic digestion and ideti fi cation of the derivatized proteins by HPLC-electrospray ionization (ESI)-MS/MS with the probability-based protein identi fi cation algorithm, identi fi ed 103 proteins in the soluble extract (10 microg protein) of Caenorhabditis elegans. Copyright (c) 2005 John Wiley & Sons, Ltd.
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[
Chembiochem,
2011]
Cyclophilin A (CypA) is a member of the immunophilin family of proteins and receptor for the immunosuppressant drug cyclosporin A (CsA). Here we describe the design and synthesis of a new class of small-molecule inhibitors for CypA that are based upon a dimedone template. Electrospray mass spectrometry is utilised as an initial screen to quantify the protein affinity of the ligands. Active inhibitors and fluorescently labelled derivatives are then used as chemical probes for investigating the biological role of cyclophilins in the nematode Caenorhabditis elegans.
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[
Biomaterials,
2010]
We have shown that platinum nanoparticle species (nano-Pt) is a superoxide dismutase/catalase mimetic that scavenges superoxide and hydrogen peroxide. In Caenorhabditis elegans, nano-Pt functions as an effective antioxidant that induces an extension in lifespan and strong resistance against excessive oxidative stress. Our study with C. elegans was the first trial to use nano-Pt as a bio-active substance. However, a high concentration of nano-Pt was required for these survival effects, probably due to limited membrane permeability. Here, we show that the conjugation of nano-Pt with an HIV-1 TAT fusion protein C-terminally linked to a peptide with high affinity for platinum improves internalization, eliciting a similar level of antioxidant effects at one hundredth the concentration of unconjugated nano-Pt. This approach is a potential method to facilitate translocation of bio-active nanoparticles into living organisms and could be a model assay for estimate the effects of antioxidant in living organism.
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Yang P, Zhong F, Liu S, Hao Y, He F, Zhu Y, Ying W, Yang D, Qian X, Lin C, Wu S, Jiang Y
[
PLoS One,
2012]
A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.
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[
International Worm Meeting,
2005]
WormBase offers many features that make it an attractive system for comparative genomics: periodic referential software and data freezes, scriptable access through feature-rich programming interfaces, a publically accessible data mining server, and user-friendly graphical interfaces. With the addition of three additional genomes in 2005, the case for WormBase as a platform for comparative genomics is even more compelling. Research areas such as comparative genomics are fueling requests for genome-wide data. To meet these requests, WormBase has added new graphical tools, released a new programmatic interface, and simplified the process of building a local installation. Graphical data mining tools at WormBase continue to evolve in response to user requests. For example, the RNAi phenotype search is now limitable by data set or by genetic or physical map position and the Batch Genes script can fetch orthology data. The most significant new graphical tool at WormBase is the recent introduction of WormMart, a highly flexible interface for retrieving annotations and sequences. We continue to expand options for users wising to programmatically access the resource, most recently with the release of the Perl Bio::GMOD module. Bio::GMOD aims to provide a unified programmatic interface to model organism databases. Thus, scripts written to fetch all of the genes from WormBase can seamlessly execute the same task at FlyBase regardless of differences in the data model or naming conventions. Furthermore, Bio::GMOD insulates end users from the complexity of the data model by translating common queries into one appropriate for the current schema. WormBase continues to offer direct programmatic access to the underlying databases through the AcePerl and Bio::DB::GFF modules, as well as providing a publically accessible data mining server at aceserver.cshl.org. We have also made it possible to run WormBase locally in your lab or university through a greatly simplified installation and update procedure. Local installations do not suffer from network latency, are less susceptible to server load, can be accessed with the WormBase data mining modules, and support viewing of local annotations side-by-side with the core WormBase data.