9 Papers found (0.009 seconds)

Binder BF et al. (1992) Journal of Agricultural and Food Chemistry "Inhibition of Development in Caenorhabditis elegans (Nematoda) by a reduced aromatic schiff base and related compounds."

Kochansky JP, Binder BF, Chitwood DJ, Demilo AB

[

Journal of Agricultural and Food Chemistry,

1992]

Insect growth regulators with dissimilar chemical structures possess biological activity in parasitic and free-living nematodes. Certain steroids inhibit growth and reproduction in Caenorhabditis elegans, Nippostrongylus brasiliensis, and Heligmosoides polygyrus (=Nematospiroides dubius). Sesquiterpenoid insect juvenile hormones and their analogs disrupt the development of a wide variety of nematodes, whereas nonterpenoid insect juvenile hormone mimics such as benzimidazoles and methoxyphenyl ethers inhibit egg hatch in the pinewood nematode, Bursaphelenchus xylophilus, and reduce growth in a goat parasite, Haemonchus contortus. The insect anti-juvenile hormone precocene II has biological activity against Caenorhabditis remanei, but its role as a nematode antihormone has not been fully clarified. The impact of these compounds on the hormonal systems in insects is fairly clear; their role as endocrine-active bioregulators in nematodes has not yet

Sousa AA et al. (2009) Ultramicroscopy "Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: implications for tomography of thick biological sections."

Leapman RD, Hohmann-Marriott MF, Zhang G, Sousa AA

[

Ultramicroscopy,

2009]

A Monte Carlo electron-trajectory calculation has been implemented to assess the optimal detector configuration for scanning transmission electron microscopy (STEM) tomography of thick biological sections. By modeling specimens containing 2 and 3at% osmium in a carbon matrix, it was found that for 1-mum-thick samples the bright-field (BF) and annular dark-field (ADF) signals give similar contrast and signal-to-noise ratio provided the ADF inner angle and BF outer angle are chosen optimally. Spatial resolution in STEM imaging of thick sections is compromised by multiple elastic scattering which results in a spread of scattering angles and thus a spread in lateral distances of the electrons leaving the bottom surface. However, the simulations reveal that a large fraction of these multiply scattered electrons are excluded from the BF detector, which results in higher spatial resolution in BF than in high-angle ADF images for objects situated towards the bottom of the sample. The calculations imply that STEM electron tomography of thick sections should be performed using a BF rather than an ADF detector. This advantage was verified by recording simultaneous BF and high-angle ADF STEM tomographic tilt series from a stained 600-nm-thick section of C. elegans. It was found that loss of spatial resolution occurred markedly at the bottom surface of the specimen in the ADF STEM but significantly less in the BF STEM tomographic reconstruction. Our results indicate that it might be feasible to use BF STEM tomography to determine the 3D structure of whole eukaryotic microorganisms prepared by freeze-substitution, embedding, and sectioning.

Xiao H et al. (2016) Chem Sci "An ultrasensitive near-infrared ratiometric fluorescent probe for imaging mitochondrial polarity in live cells and in vivo."

Tang B, Xiao H, Li P, Zhang W

[

Chem Sci,

2016]

Mitochondrial polarity is a crucial characteristic of these indispensable organelles, and tremendously impacts cellular events. Herein, we describe a new mitochondria-targeting fluorescent probe MCY-BF2 that is singularly sensitive and specifically responsive to mitochondrial polarity. The pull-push system in the conjugated structure of MCY-BF2 is responsible for the polarity-ultrasensitivity due to the excited state intramolecular charge transfer (ICT). By combining with cardiolipin, MCY-BF2 preferentially accumulates in mitochondria. Because the fluorescence emission wavelengths exhibit an obvious red-shift with increasing media polarity, the fluorescence intensity ratio at two different wavelengths versus the solvent dielectric constant can quantify the mitochondrial polarity. Experimental results demonstrate that the fluorescent intensity of MCY-BF2 in a non-polar solvent, dioxane, is 120 times higher than that in a polar solvent, dimethyl sulfoxide. As the first near-infrared (NIR) and most sensitive fluorescent imaging probe for polarity, MCY-BF2 can locate exclusively in mitochondria in various cells and discriminate polarity differences between normal and cancer cells. Also, the intrinsic polarity variance at different developmental stages in Caenorhabditis elegans (C. elegans) was reported here for the first time. Interestingly, the embryonic development stage has a more non-polar environment with a dielectric constant of 7.20, and in contrast the polarity at the young adult stage changes to 10.07. In addition, in vivo imaging results suggest that the tumor tissues of mice have an obviously lower polarity than that in normal tissues. Altogether, the merits of the NIR property, high sensitivity and moderate Stokes shift all greatly promote the accuracy of imaging. This probe will be a promising tool for studying biological processes and the pathological mechanism of polarity-related diseases.

Abbas A et al. (2018) Environ Sci Pollut Res Int "Ecotoxicological impacts of surface water and wastewater from conventional and advanced treatment technologies on brood size, larval length, and cytochrome P450 (35A3) expression in Caenorhabditis elegans."

Seitz W, Abbas A, Knopp G, Wagner M, Oehlmann J, Bollmann A, Valek L, Schulte-Oehlmann U, Schneider I

[

Environ Sci Pollut Res Int,

2018]

Anthropogenic micropollutants and transformation products (TPs) negatively affect aquatic ecosystems and water resources. Wastewater treatment plants (WWTP) represent major point sources for (micro)pollutants and TPs in urban water cycles. The aim of the current study was to assess the removal of micropollutants and toxicity during conventional and advanced wastewater treatment. Using wild-type and transgenic Caenorhabditis elegans, the endpoint reproduction, growth, and cytochrome P450 (CYP) 35A3 induction (via cyp-35A3::GFP) were assessed. Samples were collected at four WWTPs and a receiving surface water. One WWTP included the advanced treatments: ozonation followed by granular activated carbon (GAC) or biological filtration (BF), respectively. Relevant micropollutants and WWTP parameters (n=111) were included. Significant reproductive toxicity was detected for one WWTP effluent (31-83% reduced brood size). Three of four effluents significantly promoted the growth of C. elegans larvae (49-55% increased lengths). This effect was also observed for the GAC (34-41%) and BF (30%) post-treatments. Markedly, significant cyp-35A3::GFP induction was detected for one effluent before and after ozonation, being more pronounced for the ozonated samples (5- and 7.4-fold above controls). While the advanced treatments decreased the concentrations of most micropollutants, the observed effects may be attributed to effects of residual target compounds and/or compounds not included in the target chemical analysis. This highlights the need for an integrated assessment of (advanced) wastewater treatment covering both biological and chemical parameters.

Bhat VD et al. (2019) Elife "Engineering a conserved RNA regulatory protein repurposes its biological function in vivo."

Alexander JC, Fonseca DR, Tanaka Hall TM, Bhat VD, Lo TW, Campbell ZT, Shukla T, Wang Y, McCann KL, Wickens M, Qiu C

[

Elife,

2019]

PUF (PUmilio/FBF) RNA-binding proteins recognize distinct elements. In C. elegans, PUF-8 binds to an 8-nt motif and restricts proliferation in the germline. Conversely, FBF-2 recognizes a 9-nt element and promotes mitosis. To understand how motif divergence relates to biological function, we determined a crystal structure of PUF-8. Comparison of this structure to that of FBF-2 revealed a major difference in a central repeat. We devised a modified yeast 3-hybrid screen to identify mutations that confer recognition of an 8-nt element to FBF-2. We identified several such mutants and validated structurally and biochemically their binding to 8-nt RNA elements. Using genome engineering, we generated a mutant animal with a substitution in FBF-2 that confers preferential binding to the PUF-8 element. The mutant largely rescued overproliferation in animals that spontaneously generate tumors in the absence of puf-8. This work highlights the critical role of motif length in the specification of biological function.

Yang Y et al. (2015) Vet Parasitol "Screening and analysis of Hc-ubq and Hc-gst related to desiccation survival of infective Haemonchus contortus larvae."

Yang Y, Ma Y, Guo X, Du A, Chen X, Yan B

[

Vet Parasitol,

2015]

Infective Haemonchus contortus larvae (L3s) are able to protect themselves from desiccation. To explore the molecular mechanisms of desiccation survival, mRNA differential display RT-PCR was used to screen differentially expressed genes in L3s upon desiccation, followed by RNAi experiments to define gene functions. In this, 58 differentially expressed transcripts were obtained. Among these, the BF-U01A and CH-U02A fragments represent genes with the highest identity percentage in bioinformatic analysis. They were named Hc-ubq and Hc-gst based on their respective homologous ubiquitin in Caenorhabditis elegans and glutathione S-transferase in H. contortus. Quantitive RT-PCR results indicated that they were both up-regulated in desiccated L3s. Hc-ubq and Hc-gst RNAi in H. contortus showed reduced survival rate of L3s, with unchanged locomotion behavior. Homologous Ce-ubq-2 and Ce-gst-7 RNAi in C. elegans also displayed higher larval death rate. These results suggest that ubq and gst may play important roles in nematode desiccation tolerance. Our study analyzed desiccation resistance related genes in H. contortus L3s, and revealed significant research implications on the mechanisms behind nematode desiccation survival.

Khor BY et al. (2017) J Mol Graph Model "The design of target specific antibodies (scFv) by applying de novo workflow: Case study on BmR1 antigen from Brugia malayi."

Khor BY, Choong YS, Lim TS, Noordin R

[

J Mol Graph Model,

2017]

De novo approach was applied to design single chain fragment variable (scFv) for BmR1, a recombinant antigen from Bm17DIII gene which is the primary antigen used for the detection of anti-BmR1 IgG4 antibodies in the diagnostic of lymphatic filariasis. Three epitopes of the BmR1 was previously predicted form an ab initio derived three-dimensional structure. A collection of energetically favourable conformations was generated via hot-spot-centric approach. This resulted in a set of three different scFv scaffolds used to compute the high shape complementary conformations via dock-and-design approach with the predicted epitopes of BmR1. A total of 4227 scFv designs were generated where 200 scFv designs produced binding energies of less than -20 R.E.U with shape complementarity higher than 0.5. We further selected the design with at least one hydrogen bond and one salt bridge with the epitope, thus resulted in a total of 10, 1 and 19 sFv designs for epitope 1, 2 and 3, respectively. The results thus showed that de novo design can be an alternative approach to yield high affinity in silico scFv designs as a starting point for antibody or specific binder discovery processes.

Khor BY et al. (2014) Int J Mol Sci "The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches."

Noordin R, Tye GJ, Choong YS, Lim TS, Khor BY

[

Int J Mol Sci,

2014]

Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in "Brugia Rapid". However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.

Porta-de-la-Riva M et al. (2012) J Vis Exp "Basic Caenorhabditis elegans methods: synchronization and observation."

Villanueva A, Ceron J, Porta-De-La-Riva M, Fontrodona L

[

J Vis Exp,

2012]

Research into the molecular and developmental biology of the nematode Caenorhabditis elegans was begun in the early seventies by Sydney Brenner and it has since been used extensively as a model organism. C. elegans possesses key attributes such as simplicity, transparency and short life cycle that have made it a suitable experimental system for fundamental biological studies for many years. Discoveries in this nematode have broad implications because many cellular and molecular processes that control animal development are evolutionary conserved. C. elegans life cycle goes through an embryonic stage and four larval stages before animals reach adulthood. Development can take 2 to 4 days depending on the temperature. In each of the stages several characteristic traits can be observed. The knowledge of its complete cell lineage together with the deep annotation of its genome turn this nematode into a great model in fields as diverse as the neurobiology, aging, stem cell biology and germ line biology. An additional feature that makes C. elegans an attractive model to work with is the possibility of obtaining populations of worms synchronized at a specific stage through a relatively easy protocol. The ease of maintaining and propagating this nematode added to the possibility of synchronization provide a powerful tool to obtain large amounts of worms, which can be used for a wide variety of small or high-throughput experiments such as RNAi screens, microarrays, massive sequencing, immunoblot or in situ hybridization, among others. Because of its transparency, C. elegans structures can be distinguished under the microscope using Differential Interference Contrast microscopy, also known as Nomarski microscopy. The use of a fluorescent DNA binder, DAPI (4',6-diamidino-2-phenylindole), for instance, can lead to the specific identification and localization of individual cells, as well as subcellular structures/defects associated to them.