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We report design and test results of a new thermal contact method for a PrNi 5 rod, a nuclear coolant for a compact and continuous nuclear demagnetization refrigerator (CNDR) which can keep temperature below 1 mK continuously, using Zn soldering rather than Cd soldering. By measuring a residual electrical resistance of a short test piece, the thermal contact resistivity between the PrNi 5 rod and an Ag wires thermal link was estimated as 1.8 ± 0.1 × 10 - 4 T - 1 Km 2 W - 1 . Based on this value and 2D numerical and 1D analytical thermal simulations, the largest possible temperature gradient throughout the nuclear stage is calculated to be negligibly small (≤ 2 %) at 1 mK under a 10 nW heat leak, the expected cooling power of the CNDR. The whole assembly of CNDR using two PrNi 5 nuclear stages designed in this way is also outlined. [ABSTRACT FROM AUTHOR]

The structure of a protein determines its function, and the advancement of machine learning has led to the rapid development of protein structure prediction. Protein structure comparison is crucial for inferring the evolutionary relationship of proteins, drug discovery, and protein design. In this paper, we propose a multi-level visual analysis method to improve the protein structure comparison between predicted and actual structures. Our method takes the predicted results of the Recurrent Geometric Network (RGN) as the main research object and is mainly designed following three levels of protein structure visualization on RGN. Firstly, at the prediction accuracy level of the RGN, we use the Global Distance Test—Total Score (GDT_TS) as the evaluation standard, then compare it with distance-based root mean square deviation (dRMSD) and Template Modeling Score (TM-Score) to analyze the prediction characteristics of the RGN. Secondly, the distance deviation, torsion angle, and other attributes are used to analyze the difference between the predicted structure and the actual structure at the structural similarity level. Next, at the structural stability level, the Ramachandran Plot and PictorialBar combine to be improved to detect the quality of the predicted structure and analyze whether the amino acid residues conform to the theoretical configuration. Finally, we interactively analyze the characteristics of the RGN with the above visualization effects and give reasons and reasonable suggestions. By case studies, we demonstrate that our method is effective and can also be used to analyze other predictive network results. [ABSTRACT FROM AUTHOR]

Molecular cavities play a critical role in our understanding of molecular phenomena. Recently, a number of works on the visual analysis of protein cavity dynamics have been developed to allow experts and users to interactively research dynamic cavity data. However, previous explorations are limited to studying cavity-lining amino acids and they lack a consideration of the impact of the key amino acids, which are far away from the cavity but have an important impact on the cavity. When studying protein amino acids, biochemists use normal mode decomposition to analyze protein changes on a time scale. However, the high-dimensional parameter space generated via decomposition is too large to be analyzed in detail. We present a novel approach that combines cavity characterization and normal mode analysis (NMA) for cavity dynamics analysis to reduce and explore this vast space through interactive visualization. PNMAVis can analyze whether direct factors (cavity-lining amino acids) or indirect factors (key amino acids) affect cavity changes, through multiple linked 2D and 3D views. The visual analysis method we proposed is based on close cooperation with domain experts, aiming to meet their needs to explore the relationship between cavity stability and cavity-lining amino acids fluctuations and key amino acids fluctuations as much as possible, and also to help domain experts identify potential allosteric residues. The effectiveness of our new method is demonstrated by the case study conducted by cooperative protein experts on a biological field case and an open normal mode data set. [ABSTRACT FROM AUTHOR]

An important strategy for treating neurodegenerative disorders is to maintain the levels of acetylcholine in the synaptic cleft by blocking the cholinesterases. Searching for new effective compounds with inhibited acetylcholinesterase and butyrylcholinesterase activity is one of the most significant challenges of the modern scientific research. The aim of this study was the optimization of the condition for cholinesterase activity determination by high-performance liquid chromatography coupled with diode array detector (HPLC-DAD) in terms of concentrations of enzymatic reaction mixture components, temperature of incubation, and incubation time. In vitro investigation of acetylcholinesterase and butyrylcholinesterase activity inhibition by some isoquinoline alkaloids and extracts obtained from the aerial part and roots of Macleaya cordata collected in May, July, and September. Acetylcholinesterase and butyrylcholinesterase activity inhibition of the extracts obtained from the plant had not been tested previously. The application of the HPLC method allowed eliminating absorption of interfering components, for example, alkaloids such as sanguinarine and berberine. The HPLC method was successfully applied for the evaluation of the acetylcholinesterase inhibitory activity in samples such as plant extracts, especially those containing colored components adsorbing at the same wavelength as the adsorption wavelength of 5-thio-2-nitro-benzoic acid, which is the product of the reaction between thiocholine (product of the hydrolysis of acetyl/butyrylthiocholine reaction) with Ellman's reagent. Moreover, liquid chromatography coupled with a triple quadrupole mass spectrometer (LC–QqQ–ESI–MS/MS) analysis allowed evaluating the identification of relevant bioactive compounds in the obtained plant extracts. The investigated alkaloids, especially sanguinarine and chelerythrine, and all the Macleaya cordata extracts, especially the extract obtained from the aerial part collected in May, exhibited very high cholinesterase activity inhibition. HPLC-DAD was also applied for the kinetics study of the most active alkaloids sanguinarine and chelerythrine. Our investigations demonstrated that these plant extracts can be recommended for further in vivo experiments to confirm their cholinesterase inhibition activity. [ABSTRACT FROM AUTHOR]

Cytochrome P450 (CYP) enzymes are well known for metabolism of drugs. The present study attempts to understand the homotropic cooperativity of CYP3A4 inhibitor Ketoconazole (KLN) and the plasticity of the active site upon binding to different drug chemotypes. To understand this, molecular dynamic (MD) simulation studies of four systems of CYP3A4 have been undertaken followed by structural analysis of the crystallographic structures bound to five drug molecules. Unlike earlier reports, our study revealed that the region following helix F and G ‐ helix H and preceding I‐ exhibited RMSF values in the range of 4–6 Å. The binding pattern of inhibitors may involve an initial binding at the peripheral site followed by their coordination with heme. Binding of KLN at the heme binding site was energetically more stable as compared to the KLN bound at other positions. The number of non‐bonded interactions appeared to increase between the ligands and the CYP3A4 residues when both the sites were occupied. Involvement of hydrophobic residues (I300, I301, F304, A305, T309) increased during the homotropic cooperativity of ligands. Binding of the ligand at the heme binding site followed by binding at the peripheral site induces homo cooperativity effect. We also report here that 3D volume occupancy of ligands determines the phenomenon of homotropic versus non‐homotropic effect which was observed from the binding mode analysis of KLN (homotropic ligand) and Ritonavir (non‐homotropic ligand). [ABSTRACT FROM AUTHOR]

The term bioluminescence refers to a conspicuous light emission displayed by numerous aquatic and terrestrial organisms. This phenomenon has so far not been observed in several taxonomic groups like archaea, protista, platyhelminthes, chelicerata, cephalochordata, amphibians, reptiles, birds, plants, and mammals. However, some luminescent bacteria, fungi and microalgae like dinoflagellates are known. Bioluminescence has become a powerful biological tool and revolutionized several medical, physiological and biotechnological approaches, such as, for example, the study of metabolic pathways of bacteria to mammals. In 2008 O. Shimomura, M. Chalfie and R. Tsien were awarded the Chemistry Nobel prize for their discovery of the protein GFP, which is co-expressed with aequorin, the calcium-activated photoprotein involved in the bioluminescence reaction of the jellyfish Aequorea victoria. Some organisms are known to display bioluminescence only under certain kinds of stimulation and stress conditions; others appear to produce their light without prior stimulation either continuously or intermittently. Despite the discovery of more than 700 genera of bioluminescent organisms from marine, terrestrial, and freshwater environments, there is often still insufficient knowledge about their bioluminescence emission patterns under natural and stress conditions. Furthermore, there are no detailed reviews on stimulation techniques that can be used to test whether organisms previously not having been recognized to be luminescent are luminescent or not. This paper reviews various stimulants, such as chemical, mechanical, photic, thermal, magnetic and electrical ones, used in tests to elicit the emission of light in known bioluminescent organisms. This account should help researchers to extend their investigations to identify organisms hitherto not deemed to be luminescent. [ABSTRACT FROM AUTHOR]

Social media activity on a research article is considered to be an altmetric, a new measure to estimate research impact. Demonstrating software on Twitter is a powerful way to attract attention from a larger audience. Twitter integration of software can also lower the barriers to trying the tools and make it easier to save and share the output. We present three case studies of Twitter bots for cheminformatics: retrosynthetic analysis, 3D molecule viewer, and 2D chemical structure editor. These bots make software research more accessible to a broader range of people and facilitate the sharing of chemical knowledge, concepts, and ideas. [ABSTRACT FROM AUTHOR]

Introduction: Macleaya cordata (Willd) R. Br. (Papaveraceae family) is a well‐known traditional Chinese medicine used to treat muscle pain, inflamed wounds, and bee bites. Benzo[c]phenanthridine alkaloids are the main active ingredients in M. cordata. In this work, sanguinarine and chelerythrine were efficiently extracted and purified by ultrahigh‐pressure extraction (UHPE) technique and pH‐zone‐refining counter‐current chromatography (PZRCCC) from M. cordata. Objective: To develop an efficient UHPE method followed by an efficient separation technique using PZRCCC for benzo[c]phenanthridine alkaloids from the study plant species, and to evaluate the study samples for anti‐breast cancer activity. Methodology: The optimal extraction conditions were optimised as extraction pressure 200 MPa, extraction solvent 95% ethanol, solid–liquid ratio 1:30 (g/mL) and extraction time 2 min. A two‐phase n‐hexane/ethyl acetate/i‐propanol/water (1:3:1.5:4.5, v/v) solvent system was optimised with 10 mmol triethylamine in the upper phase and 10 mmol trifluoroacetic acid in lower phase in PZRCCC. The sample loading was optimised as 2.50 g. Moreover, the samples were evaluated for anti‐breast cancer activity later on. Results: The 2.50 g sample loading yielded 0.45 g of sanguinarine and 0.59 g chelerythrine in one‐step separation using PZRCCC. The anti‐breast cancer activities of sanguinarine and chelerythrine were found stronger than positive control (vincristine 5.04 μg/mL) with half‐maximal inhibitory concentration values of 0.96 and 3.00 μg/mL, respectively. Conclusion: This study showed that the established methods were efficient in extraction (UHPE) and separation (PZRCCC) of the sanguinarine and chelerythrine from M. cordata. Herein the techniques of efficient extraction of sanguinarine and chelerythrine by ultrahigh pressure extraction and separation and purification by pH‐zone‐refining counter‐current chromatography were developed. The 2.50 g sample loading yielded 0.45 g of sanguinarine and 0.59 g chelerythrine in one‐step separation using n‐hexane/ethyl acetate/i‐propanol/water (1:3:1.5:4.5, v/v) solvent system with 10 mmol triethylamine in the upper phase and 10 mmol trifluoroacetic acid in lower phase in PZRCCC. The anti‐breast cancer activities of sanguinarine and chelerythrine were found stronger than positive control. [ABSTRACT FROM AUTHOR]

Pontodrilus litoralis is a cosmopolitan littoral earthworm known to exhibit bioluminescence. Recently, a congeneric species, Pontodrilus longissimus, from Thailand was described. These species are sympatric, but their burrowing depths on Thai beaches are different. In this study, we examined the in vivo and in vitro bioluminescent properties of P. longissimus and P. litoralis. Mechanical stimulation induced in vivo luminescence in P. litoralis, as reported previously, but not in P. longissimus. In vitro cross-reaction tests between these species revealed the absence of luciferin and luciferase activities in P. longissimus. The coelomic fluid of P. litoralis had strong fluorescence that matched the spectral maximum of its bioluminescence, but the same result was not observed for P. longissimus. These results suggest that P. litoralis has luminescence abilities due to the creation of bioluminescent components (i.e., luciferin, luciferase, and light emitters). The presence of both luminous and nonluminous species in a single genus is likely widespread, but only a few examples have been confirmed. Our findings provide insight into the possible functions of bioluminescence in earthworms, such as avoiding predation by littoral earwigs. [ABSTRACT FROM AUTHOR]

The integration of proteomic, transcriptomic, and genetic variant annotation data will improve our understanding of genotype–phenotype associations. Due, in part, to challenges associated with accurate inter‐database mapping, such multi‐omic studies have not extended to chemoproteomics, a method that measures the intrinsic reactivity and potential "druggability" of nucleophilic amino acid side chains. Here, we evaluated mapping approaches to match chemoproteomic‐detected cysteine and lysine residues with their genetic coordinates. Our analysis revealed that database update cycles and reliance on stable identifiers can lead to pervasive misidentification of labeled residues. Enabled by this examination of mapping strategies, we then integrated our chemoproteomics data with computational methods for predicting genetic variant pathogenicity, which revealed that codons of highly reactive cysteines are enriched for genetic variants that are predicted to be more deleterious and allowed us to identify and functionally characterize a new damaging residue in the cysteine protease caspase‐8. Our study provides a roadmap for more precise inter‐database mapping and points to untapped opportunities to improve the predictive power of pathogenicity scores and to advance prioritization of putative druggable sites. SYNOPSIS: Multi‐omic data integration maps Chemoproteomic Detected (CpD) amino acids to genomic‐level predictions of variant pathogenicity. Highly reactive cysteine and lysine residues are enriched for high pathogenicity (CADD) scores and disease‐causing pathogenic variants. A comparison of multi‐omic mapping strategies identifies common issues with data integration, including those that result from reference sequence updates and redundancy.Chemoproteomic‐detected cysteines show no significant enrichment of disease‐associated variants in CLINVAR, whereas lysines show significant enrichment for pathogenic variants.Proof‐of‐concept functional validations reveal that chemoproteomics measures of cysteine reactivity complement genetic scores to accurately predict functional residues in the cysteine protease caspase‐8. [ABSTRACT FROM AUTHOR]

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data. [ABSTRACT FROM AUTHOR]

Rationale: Eomecon chionantha Hance (ECH), a traditional folk herb, is commonly used to treat traumatic injuries based on its analgesic and anti-inflammatory properties. Previous studies have reported that alkaloids are the major bioactive components in ECH. Therefore, identification of alkaloids from ECH contributes to the discovery of its potential active ingredients and quality control in clinic treatments. Methods: A four-step screening strategy was performed as follows. (1) Extracting the accurate masses of ions related to different molecules. (2) Screening different types of compounds using their molecular cations, protonated molecules, diagnostic product ions and fragmentation pathways. (3) Comparing the characteristic product ion formulae to obtain the type and number of substituents. (4) Using the biosynthetic pathways of isoquinoline alkaloids to determine the concentration of alkaloids. Results: Ultrahigh-performance liquid chromatography-tandem quadrupole Exactive Orbitrap mass spectrometry (UHPLC/Q-Exactive Orbitrap MS) analysis combined with the four-step screening strategy was used to profile the alkaloids in ECH. The structures of 95 alkaloids in ECH were unambiguously identified or reasonably assigned, of which 76 were reported in ECH for the first time. Six types of benzylisoquinoline alkaloids were identified in ECH: six benzyltetrahydroisoquinolines, nine protopines, five N-methyltetrahydroprotoberberines, six protoberberines, eight benzophenanthridines and sixty-one dihydrobenzophenanthridines. Conclusions: This comprehensive study identified the alkaloids in ECH, thus providing a practical reference for further research. The UHPLC/Q-Exactive Orbitrap MS method, combined with the four-step screening strategy, which was developed and successfully applied to identify the alkaloids in ECH, may also be applicable for the efficient screening of other herbal medicines [ABSTRACT FROM AUTHOR]

This work relates data from field sampling of Eisenia lucens and from laboratory-based culture. Field sampling used soil sorting and vermifuge extraction and took place in beech-dominated forests of southwest Poland. Initial work derived population estimates from four sub-communities of the forest looking for seasonal dynamics and later work employed targeted sampling in summer within rotting wood to obtain live specimens for laboratory culture. A preliminary examination within and below rotten wood during winter was also undertaken. In the laboratory, clitellate earthworms were kept at 20 °C, the substrate changed every 6 months, and the population examined. Cocoons were incubated individually at 15 °C, with number of hatchlings per cocoon and the mass of each determined. Hatchlings were grown at 15 °C in field-collected wood and compared with growth in a 1:1 volume ratio of wood and horse manure. Further hatchlings were fed with horse manure only (at 10 °C) and after 19 weeks, half were transferred to 15 °C. In the field, mature individuals varied significantly (p < 0.01) in biomass between 2 sampling sites where found, with an overall mean density across sites of 4.14 ± 3.53 m−2 with a mean biomass of 2.21 ± 1.93 g m−2. Numbers in soil varied over the sampling period, with a suggestion that this species moves from mineral soil to organic-rich dead wood as conditions permit. In summer, all life stages were recovered from rotting wood above the mineral soil. Sampling in winter found cocoons in rotting wood below snow. These hatched rapidly (within 2 weeks) when taken to the laboratory. Laboratory culture allowed maintenance of a population for 2 years. Mean cocoon mass was 50.6 mg with a mean of 2.9 hatchlings per cocoon and hatchling mass was inversely proportional to number per cocoon. Growth with 50% horse manure was significantly greater (p < 0.001) than with wood. Increased temperature from 10 to 15 °C brought more significantly (p < 0.05) rapid growth. To culture this species through its life cycle, a natural substrate is needed, but then it is necessary to acclimate the animals to something more easily obtainable. More work is needed from field sampling to fully understand the seasonal dynamics of this species, which utilises different parts of the soil profile throughout the year. [ABSTRACT FROM AUTHOR]

High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values from sigma-scaled electron density maps into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license. [ABSTRACT FROM AUTHOR]

The analysis of molecular cavities, which are transport pathways in protein structures, is critical to the understanding of molecular phenomena. However, this work is challenging due to the high complexity and diversity of the macromolecular shapes in dynamic processes. In this paper, we propose a novel multiscale visualization method for visualizing the interaction of protein cavities. We design a series of scales and visualizations of cavities based on both temporal and spatial perspectives to allow domain experts to process their work at any scale of semantic abstraction. These scales demonstrate the chemical and structural properties of cavities and span from a complete protein to a cavity at a specific moment in temporal and spatial dimensions. We also create a continuous interaction space for multiscale applications. Finally, the applicability of our approach is proven through experimental use cases, with cavities in proteins being visualized and analyzed in a focus-and-context manner. Our collaborating domain experts confirmed that our approach is an efficient and reliable method of analyzing cavities with great potential for large dynamic cavity data analysis. [ABSTRACT FROM AUTHOR]

Starting from a historic perspective, we discuss the use of second sound in experimental investigations of quantized vorticity and quantum turbulence in the two-fluid temperature regime of superfluid 4 He. Starting with the theoretical prediction of second sound by Tisza and Landau and its experimental discovery by Peshkov, we briefly review the pioneering experiments of Hall, Vinen and others that have contributed in an essential way to our current understanding of quantum turbulence in superfluid 4 He, with an emphasis on relevant research performed over the last two decades in our laboratory in Prague. We then propose further dedicated experiments where second sound can be used both as a generator and detector of quantum turbulence. [ABSTRACT FROM AUTHOR]

Flexural mode vibrations of miniature piezoelectric tuning forks (TFs) are known to be highly sensitive to superfluid excitations and quantum turbulence in 3He and 4He quantum fluids, as well as to the elastic properties of solid 4He, complementing studies by large scale torsional resonators. Here, we explore the sensitivity of a TF, capable of simultaneously operating in both the flexural and torsional modes, to excitations in the normal and superfluid 4He. The torsional mode is predominantly sensitive to shear forces at the sensor–fluid interface and much less sensitive to changes in the density of the surrounding fluid when compared to the flexural mode. Although we did not reach the critical velocity for the quantum turbulence onset in the torsional mode, due to its order of magnitude higher frequency and increased acoustic damping, the torsional mode was directly sensitive to fluid excitations, linked to quantum turbulence created by the flexural mode. The combination of two dissimilar modes in a single TF sensor can provide a means to study the details of elementary excitations in quantum liquids and at interfaces between solids and quantum fluid. [ABSTRACT FROM AUTHOR]

Outer membranes are a crucial component of Gram‐negative bacteria, containing standard lipids in their inner leaflet, lipopolysaccharides (LPSs) in their outer leaflet, and transmembrane β‐barrels known as outer membrane proteins (OMPs). OMPs regulate functions such as substrate transport and cell movement, while LPSs act as a protective barrier for bacteria and can cause toxic reactions in humans. However, the experimental study of outer membranes is challenging. Molecular dynamics simulations are often used for the computational study of membrane systems, but the preparation of complex, LPS‐rich outer membranes is not straightforward. The Gram‐Negative Outer Membrane Modeler (GNOMM) is an automated pipeline for preparing simulation systems of OMPs embedded in LPS‐containing membranes in four different force fields. Given the physiological and clinical importance of outer membranes and their components, GNOMM can be a useful tool in the study of their structure, function, and implications in diseases. GNOMM is available at http://bioinformatics.biol.uoa.gr/GNOMM. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We present preliminary results of the visualization of a submerged coflow jet of liquid helium produced by a fountain pump. The jet propagating inside the bulk superfluid is visualized with particle tracking velocimetry using hydrogen particles. We compare the characteristics of the coflow jet with those measured in classical fluids such as helium gas or water. In contrast to the classical experiments, a temperature-dependent angle of the jet is observed, suggesting that the flow may not be described quasi-classically, despite the strong coupling between normal and superfluid components by mutual friction. We report on the statistics of the velocities inferred from the particle trajectories recorded by a high-speed camera at 1.68 and 1.95 K, for jet velocities ranging from 47 to 4500 mm/s. [ABSTRACT FROM AUTHOR]

A wide variety of marine bioluminescent organisms emit light via the excited‐state coelenteramide, which is produced from the coelenterazine oxidation via a series of complicated chemical reactions in protein. Photoluminescence of coelenteramide is a simple way to produce light without experiencing the intricate reactions starting from coelenterazine. To extend the color range of light emission, many coelenterazine analogues were synthesized, but mostly only produce blue and cyan fluorescence. Based on the 42 synthesized coelenterazine analogues, we theoretically studied the absorption and fluorescence properties of the corresponding coelenteramide analogues. The electronic effect, steric effect, conjugated effect and solvated effect were considered. The results indicated that conjugated effect has great influence on the strength and wavelength of fluorescence and large electron transfer is beneficial to redshift. Based on the regularities, we theoretically designed six coelenteramide analogues, and together with the original coelenteramide, the seven‐ones emit the seven colors of rainbow via their photoluminescences. This study expands the coelenteramide fluorescence to the whole visible light region and could inspire new application. This figure shows that the theoretically designed six coelenteramide analogues, D‐1‐n, D‐2‐n, D‐3‐n, D‐1‐a, D‐2‐a and D‐3‐a, together with the original coelenteramide anion, the seven coelenteramides roughly emit the seven colors of rainbow via their photoluminescences. [ABSTRACT FROM AUTHOR]

The results of a comparative study of the luciferin–luciferase systems of seven species of bioluminescing oligochaetes—Henlea petushkovi, Henlea rodionovae, Fridericia heliota (Enchytraeidae), Microscolex phosphoreus (Acanthodrilidae), Pontodrilus litoralis (Megascolecidae), Eisenia lucens, and Avelona ligra (Lumbricidae)—are presented. [ABSTRACT FROM AUTHOR]

Fc glycosylation of human immunoglobulins G (IgGs) is essential for their structural integrity and activity. Interestingly, the specific nature of the Fc glycoforms is known to modulate the IgG effector function and inflammatory properties. Indeed, while core-fucosylation of IgG Fc-glycans greatly affects the antibody-dependent cell-mediated cytotoxicity function, with obvious repercussions in the design of therapeutic antibodies, sialylation can reverse the antibody inflammatory response, and galactosylation levels have been linked to aging, to the onset of inflammation, and to the predisposition to rheumatoid arthritis. Within the framework of a structure-to-function relationship, we have studied the role of the N -glycan sequence on its intrinsic conformational propensity. Here we report the results of a systematic study, based on extensive molecular dynamics simulations in excess of 62 μs of cumulative simulation time, on the effect of sequence on the structure and dynamics of increasingly larger, complex biantennary N-glycoforms isolated from the protein, i.e. from chitobiose to the larger N -glycan species commonly found in the Fc region of human IgGs. Our results show that while core fucosylation and sialylation do not affect the intrinsic dynamics of the unlinked N -glycans, galactosylation of the α(1–6) arm shifts dramatically its conformational equilibrium from an outstretched to a folded conformation. These findings are in agreement with and can help rationalize recent experimental evidence showing a differential recognition of positional isomers in glycan array data and also the preference of sialyltransferase for the more accessible, outstretched α(1–3) arm in both isolated, and Fc-bound N -glycans. [ABSTRACT FROM AUTHOR]

Mammalian glycosaminoglycans are linear complex polysaccharides comprising heparan sulfate, heparin, dermatan sulfate, chondroitin sulfate, keratan sulfate and hyaluronic acid. They bind to numerous proteins and these interactions mediate their biological activities. GAG–protein interaction data reported in the literature are curated mostly in MatrixDB database (http://matrixdb.univ-lyon1.fr/). However, a standard nomenclature and a machine-readable format of GAGs together with bioinformatics tools for mining these interaction data are lacking. We report here the building of an automated pipeline to (i) standardize the format of GAG sequences interacting with proteins manually curated from the literature, (ii) translate them into the machine-readable GlycoCT format and into SNFG (Symbol Nomenclature For Glycan) images and (iii) convert their sequences into a format processed by a builder generating three-dimensional structures of polysaccharides based on a repertoire of conformations experimentally validated by data extracted from crystallized GAG–protein complexes. We have developed for this purpose a converter (the CT23D converter) to automatically translate the GlycoCT code of a GAG sequence into the input file required to construct a three-dimensional model. [ABSTRACT FROM AUTHOR]

Abstract: Epidemic dropsy is a potentially life‐threatening condition resulting from the ingestion of argemone oil derived from the seeds of Argemone mexicana Linn. Exposure to argemone oil is usually inadvertent, arising from mustard cooking oil adulteration. Sanguinarine, an alkaloid present in argemone oil, has been postulated as a causative agent with the severity of epidemic dropsy correlating with plasma sanguinarine levels. Cases of epidemic dropsy have also been reported following the topical application of argemone containing massage oil. Black salve, a topical skin cancer therapy also contains sanguinarine, but at significantly higher concentrations than that reported for contaminated massage oil. Although not reported to date, a theoretical risk therefore exists of black salve inducing epidemic dropsy. This literature review explores the presentation and pathophysiology of epidemic dropsy and assesses the risk of it being induced by black salve. [ABSTRACT FROM AUTHOR]

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopla during a bioluminescent swarm in Ferry Reach, Bermuda. Using the well-characterized luciferase gene of the Japanese syllid Odontosyllis undecimdonta as a reference, a complete best-matching luciferase open reading frame (329 amino acids in length) was found in all three individuals analyzed in addition to numerous other paralogous sequences in this new gene family. No photoproteins were detected. We also recovered a predicted homolog of 4-coumarate-CoA ligase (268 amino acids in length) that best matched luciferase of the firefly Luciola with the best predicted template being the crystal structure of luciferase for Photinus pyralis, the common eastern firefly. A wide variety of genes associated with periodicity were recovered including predicted homologs of clock, bmal1, period, and timeless. Several genes corresponding to putative epitoky-related changes of the eyes were recovered including predicted homologs of a phototransduction gene, a retinol dehydrogenase and carotenoid isomerooxygenase as well as a visual perception related retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase. Genes correlating to putative epitoky-related changes of the nephridia included predicted homologs of nephrocystin-3 and an egg-release sex peptide receptor. [ABSTRACT FROM AUTHOR]

The first results of the study of chromatographic and spectral properties of the detected lowmolecular-weight activators, putative emitters in the luminescent reaction of Siberian enchytraeid Henlea sp., are presented. [ABSTRACT FROM AUTHOR]