A Study of Defensive Mechanisms Employed by Two Species of Nudibranchs using Toxicity and Unpalatability Analyses

Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays were used to examine whether accumulated compounds differ in anti-predator activity. The results of this study show increased toxicity in the mantle compared to the viscera for both species. and while both species exhibited the possibility of selective sequestration, Glossodoris vespa hinted that nudibranchs may have other methods of chemical sequestration including chemical modification that would explain why more toxic and unpalatable compounds are found in the mantle. However, there was no significant change in unpalatability between the mantle and the viscera. Finally, comparisons between genera that have mantle dermal formations along the mantle rim (Glossodoris) and those that have mantle dermal formations concentrated in the mantle horn (Ceratosoma) show that despite varying classes of dietary chemicals and selectivity of sequestration, both species exhibited a chemical arsenal in the mantle that was more toxic than dietary metabolites, suggesting that toxicity is an important part of their defensive strategy

Elaborate pupils in skates may help camouflage the eye

Author Posting. © Company of Biologists, 2019. This article is posted here by permission of Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 222 (2019): jeb195966, doi:10.1242/jeb.195966.The skate Leucoraja erinacea is a bottom-dweller that buries into the substrate with its eyes protruding, revealing elaborately shaped pupils. It has been suggested that such pupil shapes may camouflage the eye, yet this has never been tested. Here, we asked whether skate pupils dilate or constrict depending on background spatial frequency. In experiment 1, the skates' pupillary response to three artificial checkerboards of different spatial frequencies was recorded. Results showed that pupils did not change in response to spatial frequency. In experiment 2, in which skates buried into three natural substrates of different spatial frequencies, such that their eyes protruded, pupils showed a subtle but statistically significant response to changes in substrate spatial frequency. Although light intensity is the primary factor determining pupil dilation, our results show that pupils also change depending on the spatial frequency of natural substrates, which suggests that pupils may aid in camouflaging the eye.This work was funded by awards from the Marine Biological Laboratory (specifically, the Hermann Foundation Award, Joan Ruderman Fund Award, Grass Foundation Fund Award and Neal Cornell Career Development Award), as well as a University of Chicago Metcalf Fellowship to C.O.2020-01-2

Efforts to reduce impact of media variability on product quality for a commercial perfusion process

Strict control of raw materials used in bioprocesses is necessary to ensure consistent product quality. However, use of poorly characterized complex components makes achieving such strict control difficult. A strong correlation between product quality variability among bulk drug substance lots and changes in a complex medium component was observed in a commercial perfusion process. This correlation was subsequently confirmed experimentally at both large and small scales. A multifaceted strategy was applied to investigate and mitigate the impact of the media variability on product quality, which included (1) studies in small scale perfusion bioreactors; (2) development of a simple cell based assay to screen different media component lots; and (3) utilization of advanced analytical techniques to identify components that impact product quality. Small-scale perfusion bioreactors were cultured using media lots whose large-scale performance were known, and results were consistent to large-scale performance, supporting the use of small-scale cultures to resolve large-scale media effects. Given the difficulty of utilizing small-scale perfusion bioreactors to screen media lots, an effort was also made to develop a shake flask protocol capable of resolving large-scale media impact on product quality. To simplify testing even further, proteomic and metabolomic analyses through LC-MS were also performed on media and soy retains. Multivariate analysis identified a number of species that could be used as a chemical fingerprint of desirable large-scale performance, which would simplify media qualifications even further. The continued development of new platforms and assays for screening undefined components improves responsiveness to raw material variability and, in turn, enables better control of product quality of commercial products

Identification of similar regions of protein structures using integrated sequence and structure analysis tools

BACKGROUND: Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. RESULTS: Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO) ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. CONCLUSION: With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation

Azo-Dye-Functionalized Polycarbonate Membranes for Textile Dye and Nitrate Ion Removal

Challenges exist in the wastewater treatment of dyes produced by the world’s growing textiles industry. Common problems facing traditional wastewater treatments include low retention values and breaking the chemical bonds of some dye molecules, which in some cases can release byproducts that can be more harmful than the original dye. This research illustrates that track-etched polycarbonate filtration membranes with 100-nanometer diameter holes can be functionalized with azo dye direct red 80 at 1000 µM, creating a filter that can then be used to remove the entire negatively charged azo dye molecule for a 50 µM solution of the same dye, with a rejection value of 96.4 ± 1.4%, at a stable flow rate of 114 ± 5 µL/min post-functionalization. Post-functionalization, Na+ and NO3− ions had on average 17.9%, 26.0%, and 31.1% rejection for 750, 500, and 250 µM sodium nitrate solutions, respectively, at an average flow rate of 177 ± 5 µL/min. Post-functionalization, similar 50 µM azo dyes had increases in rejection from 26.3% to 53.2%. Rejection measurements were made using ultraviolet visible-light spectroscopy for dyes, and concentration meters using ion selective electrodes for Na+ and NO3− ions

Spitzer Parallax of OGLE-2018-BLG-0596: A Low-mass-ratio Planet around an M Dwarf

We report the discovery of a Spitzer microlensing planet OGLE-2018-BLG-0596Lb, with preferred planet-host mass ratio q ~ 2 × 10^(−4). The planetary signal, which is characterized by a short (~1 day) "bump" on the rising side of the lensing light curve, was densely covered by ground-based surveys. We find that the signal can be explained by a bright source that fully envelops the planetary caustic, i.e., a "Hollywood" geometry. Combined with the source proper motion measured from Gaia, the Spitzer satellite parallax measurement makes it possible to precisely constrain the lens physical parameters. The preferred solution, in which the planet perturbs the minor image due to lensing by the host, yields a Uranus-mass planet with a mass of M_p = 13.9 ± 1.6 M⊕ orbiting a mid M-dwarf with a mass of M_h = 0.23 ± 0.03 M⊙. There is also a second possible solution that is substantially disfavored but cannot be ruled out, for which the planet perturbs the major image. The latter solution yields M_p = 1.2 ± 0.2 M⊕ and M_h = 0.15 ± 0.02 M⊙. By combining the microlensing and Gaia data together with a Galactic model, we find in either case that the lens lies on the near side of the Galactic bulge at a distance D_L ~ 6 ± 1 kpc. Future adaptive optics observations may decisively resolve the major image/minor image degeneracy

Spitzer Parallax of OGLE-2018-BLG-0596: A Low-mass-ratio Planet around an M Dwarf

We report the discovery of a Spitzer microlensing planet OGLE-2018-BLG-0596Lb, with preferred planet-host mass ratio q ~ 2 × 10^(−4). The planetary signal, which is characterized by a short (~1 day) "bump" on the rising side of the lensing light curve, was densely covered by ground-based surveys. We find that the signal can be explained by a bright source that fully envelops the planetary caustic, i.e., a "Hollywood" geometry. Combined with the source proper motion measured from Gaia, the Spitzer satellite parallax measurement makes it possible to precisely constrain the lens physical parameters. The preferred solution, in which the planet perturbs the minor image due to lensing by the host, yields a Uranus-mass planet with a mass of M_p = 13.9 ± 1.6 M⊕ orbiting a mid M-dwarf with a mass of M_h = 0.23 ± 0.03 M⊙. There is also a second possible solution that is substantially disfavored but cannot be ruled out, for which the planet perturbs the major image. The latter solution yields M_p = 1.2 ± 0.2 M⊕ and M_h = 0.15 ± 0.02 M⊙. By combining the microlensing and Gaia data together with a Galactic model, we find in either case that the lens lies on the near side of the Galactic bulge at a distance D_L ~ 6 ± 1 kpc. Future adaptive optics observations may decisively resolve the major image/minor image degeneracy

Kinome and Transcriptome Profiling Reveal Broad and Distinct Activities of Erlotinib, Sunitinib, and Sorafenib in the Mouse Heart and Suggest Cardiotoxicity From Combined Signal Transducer and Activator of Transcription and Epidermal Growth Factor Receptor Inhibition

BACKGROUND: Most novel cancer therapeutics target kinases that are essential to tumor survival. Some of these kinase inhibitors are associated with cardiotoxicity, whereas others appear to be cardiosafe. The basis for this distinction is unclear, as are the molecular effects of kinase inhibitors in the heart. METHODS AND RESULTS: We administered clinically relevant doses of sorafenib, sunitinib (cardiotoxic multitargeted kinase inhibitors), or erlotinib (a cardiosafe epidermal growth factor receptor inhibitor) to mice daily for 2 weeks. We then compared the effects of these 3 kinase inhibitors on the cardiac transcriptome using RNAseq and the cardiac kinome using multiplexed inhibitor beads coupled with mass spectrometry. We found unexpectedly broad molecular effects of all 3 kinase inhibitors, suggesting that target kinase selectivity does not define either the molecular response or the potential for cardiotoxicity. Using in vivo drug administration and primary cardiomyocyte culture, we also show that the cardiosafety of erlotinib treatment may result from upregulation of the cardioprotective signal transducer and activator of transcription 3 pathway, as co-treatment with erlotinib and a signal transducer and activator of transcription inhibitor decreases cardiac contractile function and cardiomyocyte fatty acid oxidation. CONCLUSIONS: Collectively our findings indicate that preclinical kinome and transcriptome profiling may predict the cardiotoxicity of novel kinase inhibitors, and suggest caution for the proposed therapeutic strategy of combined signal transducer and activator of transcription/epidermal growth factor receptor inhibition for cancer treatment