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1,456 results for “residues”
Milkweed plants bought at nurseries may expose monarch caterpillars to harmful pesticide residues
<p>The decline of monarch butterflies in both the eastern and western United States has garnered widespread public interest. Planting milkweeds, their larval host plants, has been promoted as one action individuals can take, but little is known with respect to potential pesticide contamination of store-bought milkweeds. In this study, we collected leaf samples from 235 milkweed plants purchased at 33 retail nurseries across the US to screen for pesticides. Across all samples, we detected 61 different pesticides with an average of 12.2 (±5.0) compounds per plant. While only 9 of these compounds have been experimentally tested on monarch caterpillars, 38 % of samples contained a pesticide above a concentration shown to have a sub-lethal effect for monarchs. We detected only a modest predictive ability of retailer size and milkweed species, and plants with labels advertising their value for wildlife did not have fewer pesticides at concentrations known to have a negative effect on monarchs. These results demonstrate the extensiveness of pesticide exposure within nursery milkweeds and the potential impacts on monarchs and other insects exposed to store-bought plants.</p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Bulk stable carbon and nitrogen isotopes of food residues on pottery, stable carbon isotopes of lipids from pottery
<p>Supplementary data for Philippsen, B. (2023) Changing diet in a changing world. In: Groß, D. and Rothstein , M. (eds) Changing Identities in a Changing World.</p>
Residue Neighbours
<p>It contains the residue neighbours of the decoys</p>
Annexes on the 2021 EU report on pesticide residues
<p>Detailed information on the different control programmes, full list of samples exceeding the MRLs anonymised by sample code, analytical scope from the official laboratories reporting to EFSA data on pesticide residues, the HBGV and PF used in the risk assessment.</p> <p>Detailed information on deterministic and probabilistic risk assessment results.</p>
Pore-scale characterization of residual gas remobilization in CO2 geological storage
<p>A decrease in reservoir pressure can lead to remobilization of residually trapped CO<sub>2</sub>. In this study, the pore-scale processes related to trapped CO<sub>2</sub> remobilization under pressure depletion were investigated with the use of high-resolution 3D X-ray microtomography. The distribution of CO<sub>2</sub> in the pore space of Bentheimer sandstone was measured after waterflooding at a fluid pressure of 10 MPa, and then at pressures of 8, 6 and 5 MPa. At each stage CO<sub>2</sub> was produced, implying that swelling of the gas phase and exsolution allowed the gas to reconnect and flow. After production, the gas reached a new position of equilibrium where it may be trapped again. At the end of the experiment, we imaged the sample again after 30 hours. Firstly, the results showed that an increase in saturation beyond the residual value was required to remobilize the gas, which is consistent with earlier field-scale results. Additionally, Ostwald ripening and continuing exsolution lead to a significant change in fluid saturation: transport of dissolved gas in the aqueous phase to equilibriate capillary pressure led to reconnection of the gas and its flow upwards under gravity. The implications for CO<sub>2</sub> storage are discussed: an increase in saturation beyond the residual value is required to mobilize the gas, but Ostwald ripening in turn can allow local reconnection of hitherto trapped gas, thus enhancing migration and may reduce the amount of CO<sub>2</sub> that can be capillary trapped in storage operations.</p>
Fig. 8 in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 8. Effect of overexpression of different LjSK1 variants in L. japonicus hairy roots. Physiological parameters of L. japonicus wild type hairy roots transformed with LjSK1 variants: LjSK1 90–467 lacking the 89 N-terminal residues, LjSK1_K167A, LjSK1_Y298A, and native LjSK1 at 21 days post inoculation with rhizobium. Control roots were transformed with the empty T-DNA vector. Values shown are the average ± SEM of n = 6–16 individual hairy roots per construct. Letters above each graph indicate statistically significant differences (p <0.05) between samples using One-way ANOVA followed by Fischer's LSD post-hoc comparison.
Fig. 7 in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 7. Appearance of whole plants and nodules of L. japonicus hairy root lines transformed with the different LjSK1 variants. A, F) Control (empty vector); B, G) native LjSK1; C, H) LjSK1 K167A; D, I) LjSK1 Y298A; E, J) LjSK190-467. A-E) Representative whole plants with regenerated hairy roots. F-J) Images of nodules on regenerated hairy roots taken in bright-field (top panels) and with an RFP filter to visualize rhizobium colonisation (bottom panels). Scale bars in A-E are 5 cm and in F-G 2 mm.
Fig. 6. Western blot analysis with a p in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 6. Western blot analysis with a p-GSK-3α/β (6D3) (Santa Cruz Biotechnology, Inc.) monoclonal antibody raised against a phosphopeptide corresponding to amino acids residues surrounding Tyr279 of human GSK3α and Tyr216 of human GSK3β. Lane 1: recombinant LjSK1 and lane 2: LjSK1 Y298A variant. Both proteins have a GST-tag.
Fig. 4 in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 4. pH (A) and temperature (B) curves for LjSK1 together with standard error bars. Points represent the average value of three measurements. RLU refers to Relative Light Units and ΔRLU is for the difference between a control sample (without enzyme) and the corresponding sample with enzyme. Measurements were performed as described in section 5.3.
Fig. 2. A in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 2. A homology model of the LjSK1 – ATP complex based on the structure of human GSK3β (PDB:1J1B) (Aoki et al., 2004) after refinement with molecular dynamics simulations and docking of the ATP molecule at the ATP binding site. N- and C-terminal lobes are indicated by different colors and the G-loop and the activation loop are indicated in purple and green, respectively. Mutated residues are shown as stick models. Figure created using Pymol (DeLano, 2002). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 1. Alignment of the primary structure of LjSK1, human GSK3β and AtSK3-2. Identical residues are shown in bold. Residues mutated to alanine are boxed. Residues constituting G-loop and the activation loop are shown in grey boxes and the respective structural feature is indicated. Black arrows indicate residues predicted to be in close proximity to the phosphates of ATP. Gaps, represented by dashes, were introduced into the sequences to optimize the alignment.
Statistical error estimation from residual statistics of multiple collocated datasets: Data from synthetic experiments
<p>This archive contains the data used in the paper "How far can the statistical error estimation problem be closed by collocated data?" by A.Vogel and R.Menard (preprint available at: https://doi.org/10.5194/egusphere-2022-996) accepted for publication in Nonlinear Processes in Geophysics (NPG). </p> <p>The data refers to the synthetic experiments in Sect.5 of the paper which demonstrate the general ability to estimate statistical error covariances and cross-statistics from residual covariances, as well as the effects of inaccurate assumptions with respect to different setups.</p> <p>Further information on the data can be found in the README.txt file.</p>
Fig. 1 in A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases
Fig. 1. Involvement of N-methyltransferases in BIA biosynthesis. Coclaurine N-methyltransferase (CNMT) acts in the core BIA pathway and converts an unmethylated secondary amine to a mono-methylated tertiary amine. Reticuline N-methyltransferase (RNMT) and Pavine N-methyltransferase (PavNMT) act in several branch pathways and primarily convert mono-methylated tertiary amines into a di-methylated quaternary amines. Tetrahydroprotoberberine N-methyltransferase (TNMT) acts in other branch pathways and converts a bicyclic unmethylated tertiary amine into a quaternary amine. † denotes activities that have been demonstrated in vitro but not conclusively associated with the enzyme via in planta experimental evidence (e.g. gene silencing).
Fig. 5 in A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases
Fig. 5. Sequence-based prediction and in vivo screening of putative CNMT and RNMT enzymes. (A) The identity of residue 204 (E, glutamic acid; G, glycine) was used to predict CNMT- or RNMT-like function, respectively. (B) Overall amino acid sequence identity does not distinguish CNMT- or RNMT-like enzymes from each other (Supplementary Dataset 5). (C) Formation of N-methylated products following supplementation of yeast cultures with (S)-coclaurine (white bars), (S)-N- methylcoclaurine (black bars) and (S)-reticuline (grey bars). For each substrate, the culture with the greatest mean product concentration normalized to optical density was set to 100% and all other values were scaled accordingly (30.7μM OD−1 (S)-N-methylcoclaurine, HCANMT1; 3.4μM OD−1 (S)-N,N-dimethylcoclaurine, SCANMT1; 2.0μM OD−1 (S)-tembetarine, SCANMT1). Error bars represent standard deviation of four replicate cultures. Western blot analysis of NMT expression is show in Supplementary Fig. 6.
Fig. 3 in A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases
Fig. 3. Enzymatic activities of wild-type CNMT, wild-type RNMT and reciprocal 204 mutants. (A) Activity with canonical CNMT substrate (S)-coclaurine. Black bars indicate mono-methylated product (S)-N-methylcoclaurine and grey bars indicate di-methylated product (S)-N,N-dimethylcoclaurine. (B) Activity with tertiary amine substrate (S)-N-methylcoclaurine. (C) Activity with canonical RNMT substrate (S)-reticuline. Products were identified and quantified by LC-MS/MS. Error bars represent standard deviation of three replicates. WT denotes results corresponding to the wild-type enzyme.
Fig. 2 in A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases
Fig. 2. Analysis of key active site residues in BIA N-methyltransferases. (A) Primary sequence alignment of functionally validated BIA NMTs showing that residue 204 is conserved within BIA NMT subtypes (i.e. E in CNMTs and TNMTs, G in RNMTs, A in PavNMTs) whereas residues previously suggested to form a catalytic dyad (E207 and H208) are universally conserved. (B, C) Docking of RNMT substrate (S)-reticuline (cyan) into the active site of (B) CjCNMT (PDB 6GKV) and (C) PsRNMT (homology model) reveals a steric clash between the N-methyl group and residue E204 but not G204. S-Adenosylhomocysteine is shown in pink. Spheres represent Van der Waals radii and the distance between key atoms is given in angstroms.
Fig. 4 in A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases
Fig. 4. Superimposition of residue 204 identity on a maximum-likelihood phylogenetic analysis of N-methyltransferase gene candidates. The cladogram was adapted from that deposited in DRYAD by Hagel et al. (2015b) (https://doi.org/10.5061/dryad.bh276/18) and the corresponding sequences are described in Supplementary Dataset 4. CjCNMT was not included in the original analysis but is most similar to TfCNMT (86% amino acid identity). Key nodes are labelled with support values representing the number of 1000 bootstrapped trees in which the associated taxa clustered together. Putative BIA NMT sequences were aligned by Clustal Omega and the identity of the residue corresponding to E204 in CjCNMT was mapped onto each taxa (glutamic acid, green; glycine, purple; alanine, cyan; glutamine, yellow; serine; orange). BIA NMTs for which in vitro functional characterization data was available are indicated with black arrows and those subjected to yeast-based in vivo characterization in this work are indicated with white arrows. Prior to this report, sequence-based prediction of BIA NMT sub-functionalization was reliable for TNMT-like enzymes only due to their clustering as a single well-defined clade. CNMT-, RNMT- and PavNMT-like sequences are distributed amongst several less well-defined clades.
Influence of visual blur on Tau effect: residual attention resources overflow hypothesis
<p>Data for "Influence of visual blur on Tau effect: residual attention resources overflow hypothesis"</p>
Iterative convergent computation may not be a useful inductive bias for residual neural networks
<p>This repository contains the code and data necessary to reproduce the results and figures in "Iterative convergent computation may not be a useful inductive bias for residual neural networks".</p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.