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FIGURE 3. CMM-V-10108 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 3. CMM-V-10108, shear-fractured Miocene cetacean lumbar vertebra in three transverse CT-scan images. These CT-scan images cut through the vertebra in an anterodorsal-posteroventral direction. A. CT-scan image through the anterior portion of the vertebra showing the wide-open lumen of the shear-compression fracture. B. CT-scan image from approximately 1 cm behind A, showing the thickness of the periosteal reactive bone layer. C. CT-image at about the midpoint in the length of the vertebra showing the posterior-most part of the sheared base of the centrum compressed (telescoped) into the body of the centrum.

FIGURE 7. CMM-V-8522 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 7. CMM-V-8522, Otodus megalodon lower anterior tooth in labial view. This tooth was found touching one of the two pathological vertebrae (CMM-V-10108). Notice the spall-fracture marking the tip of the tooth. White scale bar equals 10 mm.

FIGURE 6. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 6. CMM-V-10108, a second Miocene pathological cetacean vertebra (also shown in Figure 5) associated with the one shown in Figures 2-4. A. CT-scan image towards the anterior end of the vertebra. B. CT-scan image at about the midpoint in the length of the vertebra showing the thickness of the periosteal reactive bone.

FIGURE 8 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 8. One possible way in which the shear-compression fracture occurred in CMM-V-10108. The posterior vertebral column was severely hyperflexed to such a degree that at least one of its vertebrae experienced a shear-compression fracture, and the periosteum was pulled away from most of the sides of both vertebrae. Artwork by Clarence (Shoe) Schumaker (CMM).

FIGURE 5. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 5. CMM-V-10108, a second Miocene pathological cetacean vertebra (CT-scans shown in Figure 6) associated with the one shown in Figures 2-4. A. Posterior view showing that the neural spine is incomplete and that the sides of the centrum are covered with periosteal reactive bone. B. ventral view to highlight the periosteal reactive bone. In B, the anterior end of the centrum is up.

FIGURE. 1 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE. 1. The site along Calvert Cliffs where the two pathological cetacean vertebrae (CMM-V-10108) and associated Otodus megalodon tooth (CMM-V-8522) were found in situ in Shattuck-Zone 12. Looking north along the cliffs at Warrior's Rest. Photo by M. Ellwood.

FIGURE 4. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation

FIGURE 4. CMM-V-10108, a single CT-scan image in the sagittal plane of a Miocene pathological cetacean vertebra in left lateral view showing the broken lower portion of the centrum, the displaced piece of bone, and the new bone growth (periosteal reactive bone ventrally).

Fig. 4 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)

Fig. 4 Comparisojs amojc tde jative Bt63 ajd tde referejce straij Bt-H14 tdroucd biocdemical profilijc, scajjijc electroj microcrapdu ajd pdasecojtrast microscopu. Ij a, biocdemical profilijc sitd tde API 50CH sustem sdoss tdat tde Bt63 isolate produces acid from sucrose (ijdicated bu arrow), sdereas ij b Bti-H14 is jecative (arrow); all otder 49 biocdemical reactiojs sere similar. Ij c ajd d, scajjijc electroj microcrapd (×10,000) of Bt63 reveals its larcer Cry crustals (Cr) ajd smaller spores (Sp) tdaj tdose Bti-H14. Ij e ajd f, tde pdase-cojtrast microcrapds of sucrose cradiejt-separated Cry Crustals (Cr) from Bt63 appear, comparativelu, larcer tdaj tdose of Bti-H14. Scale-bars: c, d, 1 μm; e, f, 10 μm

Fig. 3 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)

Fig. 3 SDS-PAGE profiles of sdole parasporal crustals/spores mixtures. a Profiles after dissolutioj of proteij crustals at alkalije pH (10.5–11). b Profiles follosijc pH-jeutralizatioj. c Profiles after trupsij-treatmejt (silver staij). Tde referejce Bt-H14 is labelled as Laje 15 ajd represejted jative Bt isolates labelled sitd tdeir respective idejtificatioj jumbers (see Table 4). Lajes M: proteij molecular mass markers (245 to 11 kDa). Across all tdree cojditiojs, SDS-PAGE profiles sere distijct betseej tde dicdlu bio-active jative Bt-63 isolate ajd referejce Bti-H14 sitd white ajd black arross ijdicatijc bajds presejt ij oje but jot tde otder

Fig. 1 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)

Fig. 1 Neicdbour-joijijc tree describijc tde decree of cejetic similaritu of jative larvicidal ajd joj-larvicidal (NL) isolated from Saudi Arabia, compared to sequejces from tde Bti-H14 ajd B. cereus referejce straij. Outcroups ijclude tde GRAM-positive bacteria Lysinibacillus sphaericus, Bacillus pumilus ajd B. megatorium. Bootstrap values are ijdicated as sell as isolates tdat sere sicjificajtlu more larvicidal (*), as sell as tde dicdlu letdal Bt63 isolate (**)

Fig. 2 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)

Fig. 2 Pdotocrapds of acarose electropdoresis cels (2%) for PCR-profilijc sitd a pajel of Cry, Cyt ajd Chi ceje primers. From left to ricdt ajd for all pajels: Laje 1: 100 bp ladder; Laje 2: referejce Bti-H14; Lajes 3–25: tde 23 jative Bt straijs ijdicated bu tdeir correspojdijc idejtificatioj jumbers (see Table 3). Ij a, b, d–f, all 23 jative Bt straijs ijcludijc Bti-H14 displaued positive amplificatioj of Cyt1, Cyt2, Cry4B, Cry10, Cry11, Cyt1Aa ajd Cyt2Aa. Ij c, all straijs sere positive for Cry4A except Bt63. Ij g, all Bt straijs sere PCR jecative for Chi ceje except Bt-12 ajd 55; sdereas all Bt straijs sere PCR positive for Cyt1Ab ceje, except tde jative isolates coded 67, 60, 63, 56 ajd 16

opencc-by-4.0May 2024View details →

Conformer datasets for "Equivariant Graph Neural Networks for Toxicity Prediction"

Predictive modeling of toxicity is a crucial step in the drug discovery pipeline. It can help filter out molecules with a high probability of failing in the early stages of de novo drug design. Thus, several machine learning (ML) models have been developed to predict the toxicity of molecules by combining classical ML techniques or deep neural networks with well-known molecular representations such as fingerprints or 2D graphs. But the more natural, accurate representation of molecules is expected to be defined in physical 3D space like in ab initio methods. Recent studies successfully used equivariant graph neural networks (EGNNs) for representation learning based on 3D structures to predict quantum-mechanical properties of molecules. Inspired by this, we investigated the performance of EGNNs to construct reliable ML models for toxicity prediction. We used the equivariant transformer (ET) model in TorchMD-NET for this. Eleven toxicity data sets taken from MoleculeNet, TDCommons, and ToxBenchmark have been considered to evaluate the capability of ET for toxicity prediction. Our results show that ET adequately learns 3D representations of molecules that can successfully correlate with toxicity activity, achieving good accuracies on most data sets comparable to state-of-the-art models. We also test a physicochemical property, namely, the total energy of a molecule, to inform the toxicity prediction with a physical prior. However, our work suggests that these two properties can not be related. We also provide an attention weight analysis for helping to understand the toxicity prediction in 3D space and thus increase the explainability of the ML model. In summary, our findings offer promising insights considering 3D geometry information via EGNNs and provide a straightforward way to integrate molecular conformers into ML-based pipelines for predicting and investigating toxicity prediction in physical space. We expect that in the future, especially for larger, more diverse data sets, EGNNs will be an essential tool in this domain. PAPER https://pubs.acs.org/doi/full/10.1021/acs.chemrestox.3c00032 CODE and MODELS: The conformer data sets and trained toxicity models will be published upon acceptance of this work. The code has been made available at <a href="https://github.com/jule-c/ET-Tox">https://github.com/jule-c/ET-Tox</a>, and the processed data as well as pretrained models for training and testing can be downloaded from <a href="../record/7942946">https://zenodo.org/record/7942946</a>. We can provide the full list of conformers as XYZ files upon request.

opencc-by-4.0Jun 2024View details →

Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."

<div> All data and R code for Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis. Microplastics and Nanoplastics. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>) Abstract Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus Daphnia. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in Daphnia spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment. </div>

Fig. 3 in Preliminary study of pear ester toxicity when consumed by Polistes dominula (Hymenoptera: Vespidae)

Fig. 3. Percentage of Polistes dominula that were alive, paralyzed, or dead afer ingesting <5 µL, 5–10 µL, or>10 µL of pear ester solution.

Fig. 2 in Preliminary study of pear ester toxicity when consumed by Polistes dominula (Hymenoptera: Vespidae)

Fig. 2. Mortality of different Polistes dominula castes afer ingestion of pear ester regardless of concentration (A), and mortality of wasps following ingestion of different concentrations of pear ester (B). Different letters denote significant differences among treatments at the α=0.05 confidence level.

Fig. 1 in Preliminary study of pear ester toxicity when consumed by Polistes dominula (Hymenoptera: Vespidae)

Fig. 1. Wasp feeding arenas constructed from plastic snap caps (length 5 cm, diameter 3 cm). Each snap cap held a single wasp (Polistes dominula), which had exclusive access to a pear ester feeding solution. The solution was administered via a 77.86 microliter glass capillary tube (length 75 mm, inner distance 1.1-1.2 mm) heated over a flame and bent into a j-shape. The glass capillary tube was held in place by a firm cotton plug stopper with a slit cut into one side.

Figure 2 in Toxicity and larvicidal activity on Aedes aegypti of citronella essential oil submitted to enzymatic esterification

Figure 2. Mortality percentage of Artemia salina nauplii in relation to increased sample concentration.

Figure 1 in Toxicity and larvicidal activity on Aedes aegypti of citronella essential oil submitted to enzymatic esterification

Figure 1. Kinetics of citronellyl and geranyl cinnamates production (molar ratio alcohol/acid 3:1, enzyme 15 wt%, temperature 70°C, 150 rpm).

opencc-by-4.0Oct 2017View details →

Figure 1 in Testing the Temporal Limits of Lures and Toxicants for Trapping Fruit Flies (Diptera: Tephritidae): Additional Weathering Studies of Solid Bactrocera and Zeugodacus Male Lures and Associated Insecticidal Strips

Figure 1. Captures of Zeugodacus cucurbitae males in Jackson traps containing toxicants of variable age deployed at Aloun Farm, Oahu, Hawaii. The lures were fresh in all traps and were prepared in Hawaii at the start of the test. Two fresh toxicants were included: naled in liquid CL (bar labelled L) and a DDVP strip with a CL plug (bar labelled P). The DDVP strips weathered in Arizona and Florida were tested during the same 1-day period (December 9–10, 2015). Values represent means (+ 1 SE); 12 traps were deployed per treatment. Bars marked by different letters were significantly different (Student-Newman-Keuls multiple comparisons test).