Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Probing protein secondary structure and conformational heterogeneity.

Time-resolved and steady-state fluorescence spectroscopy in conjunction with circular dichroism were employed to investigate secondary and tertiary structural features of proteins. Several single tryptophan (Trp) proteins with known crystal structures were examined both in solution and in the crystalline state. The three neurotoxins, $\alpha$-bungarotoxin, $\alpha$-cobratoxin and erabutoxin b, consist primarily of antiparallel $\beta$-sheet and contain a number of structurally important disulphide bridges. In each case, the Trp residue is situated approximately in the centre of a $\beta$-sheet. Complete random coil secondary structure for these proteins could be facilitated via the reduction and carboxymethylation or amidocarboxymethylation of the disulphide residues. Concurrent studies, by time-resolved fluorescence and circular dichroism, of these proteins at varied denaturant concentrations showed time-resolved fluorescence provides a highly sensitive probe of local secondary structure. Time-resolved fluorescence measurements for erabutoxin b single crystals exhibited multiexponential decay kinetics (single Trp residue). The relative proportion of each decay time component was found to be dependent upon the angular orientation of the protein crystal, with respect to the vertical polarization of the incident laser beam. These experimental data provide evidence for Trp side chain rotamers in the protein crystal. Model functions, which simulated the orientational dependence of the decay component relative proportions, were consistent with this rationalization. These results are the first direct experimental evidence obtained by fluorescence, to confirm the "rotamer" model for the interpretation of Trp fluorescence decay in solution. The measurement of crotonase, apoazurin and holoazurin crystals which display a range of exponential decay kinetics, provide further evidence for Trp rotamers in single protein crystals

Exposure to Sub-lethal 2,4-Dichlorophenoxyacetic Acid Arrests Cell Division and Alters Cell Surface Properties in Escherichia coli

Escherichia coli is a robust, easily adaptable and culturable bacterium in vitro, and a model bacterium for studying the impact of xenobiotics in the environment. We have used correlative atomic force – laser scanning confocal microscopy (AFM-LSCM) to characterize the mechanisms of cellular response to the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). One of the most extensively used herbicides world-wide, 2,4-D is known to cause hazardous effects in diverse non-target organisms. Sub-lethal concentrations of 2,4-D caused DNA damage in E. coli WM1074 during short exposure periods which increased significantly over time. In response to 2,4-D, FtsZ and FtsA relocalized within seconds, coinciding with the complete inhibition of cell septation and cell elongation. Exposure to 2,4-D also resulted in increased activation of the SOS response. Changes to cell division were accompanied by concomitant changes to surface roughness, elasticity and adhesion in a time-dependent manner. This is the first study describing the mechanistic details of 2,4-D at sub-lethal levels in bacteria. Our study suggests that 2,4-D arrests E. coli cell division within seconds after exposure by disrupting the divisome complex, facilitated by dissipation of membrane potential. Over longer exposures, 2,4-D causes filamentation as a result of an SOS response to oxidative stress induced DNA damage

Deconstructing and reconstructing the yeast cell wall: A top-down, bottom-up approach

International audienceModels of the Saccharomyces cerevisiae cell wall include a complex interplay of polysaccharides and proteins, with -1,3- and --1,6- glucans representing major components in terms of dry mass. The cell wall network is decorated with proteins bound to the glucans through different types of molecular interactions, including modified GPI-anchors. Chitin is another key component, which appears at the inner surface and is concentrated in bud scars, while the outer surface is coated with mannoproteins. There is a great body of evidence supporting such models; however, the precise contribution of each molecular component to the overall cell wall viscoelasticity and integrity is still an area of active investigation. The aim of this work was to examine the structural and physical properties of the S. cerevisiae cell wall during its enzymatic degradation and subsequent regeneration, using atomic force microscopy (AFM) quantitative (QI™) and high-speed (HS) imaging. We studied a wild-type strain and two well characterized cell wall mutants of S. cerevisiae, kre6, deleted in a gene required for -1,6-glucan synthesis and knr4, deprived of a cell wall signaling protein notably involved in the transcriptional control of chitin synthase genes. Clear differences between the mutant and wild type cell walls were already distinguishable by phase contrast microscopy. Spheroplasts of each strain were prepared using zymolyase and lyticase, but imaging of the perfectly round spheroplasts proved challenging, even when housed in the wells of plasma-treated PDMS stamps coated with Cell Tak. Here we present HS- and QI-AFM imaging of S. cerevisiae exposed to lyticase, showing changes to cell wall structure and physical properties in real time.References1-F. M. Klis, A. Boorsma, P. W. J. DeGroot, Journ. Yeast 23, 185 (2006).2-B. P. Reference, Rev. Name 76, 7648 (2005).Corresponding author email: [email protected]

Near Field infrared spectroscopy of Saccharomyces cerevisiae cell walls.Authors: Gorkem Bakir, Tanya Dahms, Hélène Martin-Yken, Hans A. Bechtel, Kathleen M. Gough.

International audienc

<i>Saccharomyces cerevisiae</i> CellWall Remodeling in the Absence of Knr4 and Kre6 Revealed by Nano-FourierTransform Infrared Spectroscopy

International audienceThe cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3and β-1,6glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Nearfield Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knockout collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3-10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ∼25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior

Cinnamomum zeylanicum bark essential oil induces cell wall remodelling and spindle defects in Candida albicans

Abstract Background Cinnamon (Cinnamomum zeylanicum) bark extract exhibits potent inhibitory activity against Candida albicans but the antifungal mechanisms of this essential oil remain largely unexplored. Results We analyzed the impact of cinnamon bark oil on C. albicans RSY150, and clinical strains isolated from patients with candidemia and candidiasis. The viability of RSY150 was significantly compromised in a dose dependent manner when exposed to cinnamon bark oil, with extensive cell surface remodelling at sub inhibitory levels (62.5 μg/mL). Atomic force microscopy revealed cell surface exfoliation, altered ultrastructure and reduced cell wall integrity for both RSY150 and clinical isolates exposed to cinnamon bark oil. Cell wall damage induced by cinnamon bark oil was confirmed by exposure to stressors and the sensitivity of cell wall mutants involved in cell wall organization, biogenesis, and morphogenesis. The essential oil triggered cell cycle arrest by disrupting beta tubulin distribution, which led to mitotic spindle defects, ultimately compromising the cell membrane and allowing leakage of cellular components. The multiple targets of cinnamon bark oil can be attributed to its components, including cinnamaldehyde (74%), and minor components (< 6%) such as linalool (3.9%), cinamyl acetate (3.8%), α-caryophyllene (5.3%) and limonene (2%). Complete inhibition of the mitotic spindle assembly was observed in C. albicans treated with cinnamaldehyde at MIC (112 μg/mL). Conclusions Since cinnamaldehyde disrupts both the cell wall and tubulin polymerization, it may serve as an effective antifungal, either by chemical modification to improve its specificity and efficacy or in combination with other antifungal drugs

Rhizobium leguminosarum bv. viciae 3841 Adapts to 2,4-Dichlorophenoxyacetic Acid with "Auxin-Like" Morphological Changes, Cell Envelope Remodeling and Upregulation of Central Metabolic Pathways.

There is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), as one of the most widely applied pesticides in the world, is one such example. This herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unknown. In this study, we have used Rhizobium leguminosarum bv. viciae 3841 (Rlv) as a nitrogen fixing, beneficial model soil organism to characterize the effects of 2,4-D. Using metabolomics and advanced microscopy we determined specific target pathways in the Rlv metabolic network and consequent changes to its phenotype, surface ultrastructure, and physical properties during sublethal 2,4-D exposure. Auxin and 2,4-D, its structural analogue, showed common morphological changes in vitro which were similar to bacteroids isolated from plant nodules, implying that these changes are related to bacteroid differentiation required for nitrogen fixation. Rlv showed remarkable adaptation capabilities in response to the herbicide, with changes to integral pathways of cellular metabolism and the potential to assimilate 2,4-D with consequent changes to its physical and structural properties. This study identifies biomarkers of 2,4-D in Rlv and offers valuable insights into the mode-of-action of 2,4-D in soil bacteria