Preparation of ER Microsomes from Arabidopsis thaliana

Microsomes are vesicles derived from the endoplasmic reticulum (ER) when cells are broken down in the lab. These microsomes are a valuable tool to study a variety of ER functions such as protein and lipid synthesis in vitro.Here we describe a protocol to isolate ER-derived microsomes Arabidopsis thaliana seedlings and exemplify the use of these purified microsomes in enzyme assays with the auxin precursors tryptophan (Trp) or indole-3-pyruvic acid (IPyA) to quantify auxin synthetic capacity in microsomal and cytosolic fractions.

Pyrimidine-morpholine hybrids as potent druggable therapeutics for Alzheimer's disease: Synthesis, biochemical and in silico analyses

The identification of effective and druggable cholinesterase inhibitors to treat progressive neurodegenerative Alzheimer's disorder remains a continuous drug discovery hunt. In this perspective, the present study investigates the design and discovery of pyrimidine-morpholine hybrids (5a-l) as potent cholinesterase inhibitors. Palladium-catalyzed Suzuki-Miyaura cross-coupling reaction was employed to introduce the structural diversity on the pyrimidine heterocyclic core. A range of commercially available boronic acids was successfully coupled showing a high functional group tolerance. In vitro cholinesterase inhibitory potential using Ellman's method revealed significantly strong potency. Compound 5h bearing a meta-tolyl substituent at 2-position of pyrimidine ring emerged as a lead candidate against AChE with an inhibitory potency of 0.43 ± 0.42 µM, ∼38-fold stronger value than neostigmine (IC50 = 16.3 ± 1.12 µM). Compound 5h also showed the lead inhibition against BuChE with an IC50 value of 2.5 ± 0.04 µM. The kinetics analysis of 5h revealed the non-competitive mode of inhibition against AChE whereas computational modelling results of potent leads depicted diverse contacts with the binding site amino acid residues. Molecular dynamics simulations revealed the stability of biomolecular system, while, ADME analysis demonstrated druglikeness behaviour of potent compounds. Overall, the investigated pyrimidine-morpholine scaffold presented a remarkable potential to be developed as efficacious anti-Alzheimer's drugs.

P450 in C-C coupling of cyclodipeptides with nucleobases

Bacterial cytochrome P450 enzymes catalyze various and often intriguing tailoring reactions during the biosynthesis of natural products. In contrast to the majority of membrane-bound P450 enzymes from eukaryotes, bacterial P450 enzymes are soluble proteins and therefore represent excellent candidates for in vitro biochemical investigations. In particular, cyclodipeptide synthase-associated cytochrome P450 enzymes have recently gained attention due to the broad spectrum of reactions they catalyze, i.e. hydroxylation, aromatization, intramolecular C-C bond formation, dimerization, and nucleobase addition. The latter reaction has been described during the biosynthesis of guanitrypmycins, guatrypmethines and guatyromycines in various Streptomyces strains, where the nucleobases guanine and hypoxanthine are coupled to cyclodipeptides via C-C, C-N, and C-O bonds. In this chapter, we provide an overview of cytochrome P450 enzymes involved in the C-C coupling of cyclodipeptides with nucleobases and describe the protocols used for the successful characterization of these enzymes in our laboratory. The procedure includes cloning of the respective genes into expression vectors and subsequent overproduction of the corresponding proteins in E. coli as well as heterologous expression in Streptomyces. We describe the purification and in vitro biochemical characterization of the enzymes and protocols to isolate the produced compounds for structure elucidation.

The revealing of a novel double bond reductase related to perilla ketone biosynthesis in Perilla frutescens

BACKGROUND

Perilla frutescens is widely used as both a medicine and a food worldwide. Its volatile oils are its active ingredients, and, based on the different volatile constituents, P. frutescens can be divided into several chemotypes, with perilla ketone (PK) being the most common. However, the key genes involved in PK biosynthesis have not yet been identified.

RESULTS

In this study, metabolite constituents and transcriptomic data were compared in leaves of different levels. The variation in PK levels was the opposite of that of isoegoma ketone and egoma ketone in leaves at different levels. Based on transcriptome data, eight candidate genes were identified and successfully expressed in a prokaryotic system. Sequence analysis revealed them to be double bond reductases (PfDBRs), which are members of the NADPH-dependent, medium-chain dehydrogenase/reductase (MDR) superfamily. They catalyze the conversion of isoegoma ketone and egoma ketone into PK in in vitro enzymatic assays. PfDBRs also showed activity on pulegone, 3-nonen-2-one, and 4-hydroxybenzalacetone. In addition, several genes and transcription factors were predicted to be associated with monoterpenoid biosynthesis, and their expression profiles were positively correlated with variations in PK abundance, suggesting their potential functions in PK biosynthesis.

CONCLUSIONS

The eight candidate genes encoding a novel double bond reductase related to perilla ketone biosynthesis were identified in P. frutescens, which carries similar sequences and molecular features as the MpPR and NtPR from Nepeta tenuifolia and Mentha piperita, respectively. These findings not only reveal the pivotal roles of PfDBR in exploring and interpreting PK biological pathway but also contribute to facilitating future studies on this DBR protein family.

Bioremediation of reactive orange 16 by industrial effluent-adapted bacterial consortium VITPBC6: process optimization using response surface methodology (RSM), enzyme kinetics, pathway elucidation, and detoxification

Textile effluent is one of the most hazardous industrial pollutant sources. It is generated in huge volumes and contains a wide array of toxicants. Reactive azo dyes, which are xenobiotic compounds, are predominantly utilized by textile industries for dyeing cotton, viscose, wool, and silk. The conventional physicochemical treatments used by industrial effluent treatment plants are ineffective in dye degradation. The present study thus attempted to find a potential treatment for reactive azo dyes. A novel bacterial consortium VITPBC6 was constructed with the most potent and compatible reactive orange 16 (RO-16) decolorizing isolates of tannery and textile effluents, and the isolates were identified as Bacillus flexus VITSP6, Bacillus paraflexus VITSPB7, Bacillus megaterium VITSPB9, Bacillus firmus VITEPB1, B. flexus VITEPB2, and Bacillus aryabhattai VITEPB3. The physicochemical factors of RO-16 decolorization were optimized by response surface methodology. Consortium VITPBC6 was able to tolerate a high concentration of RO-16 up to 800 mg L^-1. A cocktail of enzymes including azoreductase, tyrosinase, laccase, lignin peroxidase, and manganese peroxidase was involved in RO-16 degradation by VITPBC6. Consortium VITPBC6 degraded RO-16 following zero-order reaction. The enzymes of consortium VITPBC6 had a V_max of 352 mg L^-1 day^-1 for RO-16 degradation; however, the K_m value was high. VITPBC6 biodegraded RO-16 resulting in the formation of small aromatic compounds. Lastly, different toxicity assays conducted with untreated RO-16 and its corresponding biodegraded metabolite revealed that the toxicity of biodegraded metabolites was significantly lower than the untreated dye.

Need for Methods to Investigate Endocannabinoid Signaling

Endocannabinoids (eCBs) are endogenous lipids able to bind to cannabinoid receptors, the primary molecular targets of the cannabis (Cannabis sativa) active principle Δ⁹-tetrahydrocannabinol. During the last 20 years, several N-acylethanolamines and acylesters have been shown to act as eCBs, and a complex array of receptors, metabolic enzymes, and transporters (that altogether form the so-called "eCB system") has been shown to finely tune their manifold biological activities. It appears now urgent to develop methods and protocols that allow to assay in a specific and quantitative manner the distinct components of the eCB system and that can properly localize them within the cell. A brief overview of eCBs and of the proteins that bind, transport, and metabolize these lipids is presented here, in orderto put in a better perspective, the relevance of methodologies that help to disclose molecular details of eCB signaling in health and disease. Proper methodological approaches form also the basis for a more rationale and effective drug design and therapeutic strategy to combat human disorders.

Measurement of lysosomal enzyme activities: A technical standard of the American College of Medical Genetics and Genomics (ACMG)

Assays that measure lysosomal enzyme activity are important tools for the screening and diagnosis of lysosomal storage disorders (LSDs). They are often ordered in combination with urine oligosaccharide and glycosaminoglycan analysis, additional biomarker assays, and/or DNA sequencing when an LSD is suspected. Enzyme testing in whole blood/leukocytes, serum/plasma, cultured fibroblasts, or dried blood spots demonstrating deficient enzyme activity remains a key component of LSD diagnosis and is often prompted by characteristic clinical findings, abnormal newborn screening, abnormal biochemical findings (eg, elevated glycosaminoglycans), or molecular results indicating pathogenic variants or variants of uncertain significance in a gene associated with an LSD. This document, which focuses on clinical enzyme testing for LSDs, provides a resource for laboratories to develop and implement clinical testing, to describe variables that can influence test performance and interpretation of results, and to delineate situations for which follow-up molecular testing is warranted.

Nanoarmored Multi-Enzyme Cascade Catalysis

This chapter reports a single-step preparation of nanoarmored bi-enzyme systems assembled on 1-D and 2-D nanomaterials, with glucose oxidase and peroxidase enzymes as model systems for cascade bio-catalysis. This is a simple and facile method to both exfoliate the bulk 1D (carbon nanotubes, CNT) and 2D nanomaterials (α-Zirconium phosphate, α-ZrP) and bind the enzymes in a single step. Exfoliation of the bulk material enhances the accessible surface area of the materials for the enzyme binding, and it also boosts the diffusion of reagents from the bulk phase to the active sites of the bio-catalysts. For example, a mixture of horseradish peroxidase, glucose oxidase, and bovine serum albumin (BSA) were adsorbed on the surfaces of the α-ZrP nanoplates or carbon nanotubes (CNT) as the bulk materials are exfoliated simultaneously, in a one-step process. The resulting bio-catalysts were thoroughly characterized by powder X-ray diffraction, electron microscopy, biochemical and biophysical methods, while enzyme activity studies proved successful binding of enzymes with retention of activities or even enhancements in their specific activities. For example, GOx/HRP/BSA/CNT displayed 6 times the activity of a mixture of GOx/HRP/BSA, under otherwise identical conditions. Similarly, GOx/HRP/BSA/ZrP had 3.5 times the activity of the corresponding mixture of GOx/HRP/BSA, in the absence of the nanoplates. These robust nano-dispersions worked extraordinarily well as active bio-catalysts. These two kinds of fabricated biocatalyst dispersions are also highly stable.

Phenotypic profile of Aedes albopictus (Skuse) exposed to pyrethroid-based mat vaporizers and underlying detoxification mechanisms: A statewide report in Selangor, Malaysia

This study examines the biological efficacy of four mosquito mat vaporizers each containing different active ingredients: prallethrin with PBO, dimefluthrin, prallethrin, and d-allethrin. The glass chamber assay was used to evaluate their efficacy on Aedes albopictus (Skuse) (Diptera: Culicidae) from nine districts in Selangor, Malaysia. Aedes albopictus exhibited different knockdown rates, with 50% knockdown times, KT₅₀, varying from 1.19 to 2.00 min, 1.22 to 2.20 min, 1.39 to 5.85 min, and 1.39 to 1.92 min for prallethrin with PBO, dimefluthrin, prallethrin and d-allethrin, respectively. In general, all populations of Ae. albopictus were completely knocked down after exposure to all active ingredients except Hulu Selangor population, which showed 96.00% knockdown against d-allethrin. On the contrary, mortality rates were observed from 84.00-100.00%, 84.00-100.00%, 90.67-100.00% and 90.67-100.00% in populations tested with prallethrin with PBO, dimefluthrin, prallethrin and d-allethrin, respectively. Moreover, significant correlations between mortality rates of prallethrin with PBO vs dimefluthrin (r = 0.836, P = 0.003), prallethrin with PBO vs prallethrin (r = 0.760, P = 0.011), and prallethrin vs d-allethrin (r = 0.694, P = 0.026) were also observed, suggesting cross-resistance among pyrethroids. d-allethrin was found to be high in insecticidal activity, followed by prallethrin, prallethrin with PBO, and dimefluthrin. In consistent with mortality due to insecticide exposure, elevated levels of enzyme activities were also demonstrated in Sabak Bernam, Hulu Selangor, Gombak, Petaling, Hulu Langat and Klang populations.

Red and white muscle proportions and enzyme activities in mesopelagic sharks

In the last decade, there has been an increase in the study of the ecology of deep-sea organisms. One way to understand an organism's ecology is the study of its metabolism. According to literature, deep-sea sharks possess a lower anaerobic enzyme activity than their shallow-water counterparts, but no difference has been observed regarding their aerobic enzyme activities. These studies have suggested deep-sea sharks should be slow and listless swimmers. However, other studies based on video observations have revealed differences in cruise swimming speed between different species. The present study examined muscles of squaliform sharks, including both luminous and non-luminous species. We combined measurements of the relative amounts of red and white muscle with assays of enzymes that are used as markers for aerobic (citrate synthase, malate dehydrogenase) and anaerobic (lactate dehydrogenase) metabolism, searching for a relationship with cruising speeds. Non-luminous deep-sea species displayed lower aerobic enzyme activities but similar anaerobic enzyme activities than the benthic shallow-water counterpart (Squalus acanthias). Conversely, luminous Etmopteridae species were found to have similar aerobic enzyme activities to S. acanthias but displayed lower anaerobic enzyme activities. Analyses revealed that red muscle proportion and aerobic enzyme activities were positively related to the cruise swimming speed. In contrast, Dalatias licha, which swims at the slowest cruise swimming speed ever recorded, presented a very low aerobic metabolic phenotype (lower aerobic marker enzymes and less red muscle). Finally, the values obtained for white muscle proportion and anaerobic metabolic phenotype suggested a high burst capacity for D. licha and non-luminous sharks.

Functional analysis of PpRHM1 and PpRHM2 involved in UDP-l-rhamnose biosynthesis in Prunus persica

UDP-l-rhamnose (UDP-Rha) is an important sugar donor for glycosylation of various cell molecules in plant. Rhamnosides are widely present in different plant tissues and play important biological roles under different developmental or environmental conditions. However, enzymes involved in UDP-Rha biosynthesis and their encoding genes have been identified in few plants, which limits the functional analysis of plant rhamnosides. Here, two UDP-Rha biosynthesis genes, named PpRHM1 (2028 bp) and PpRHM2 (2016 bp), were isolated and characterized from Prunus persica, which is rich sources of flavonol rhamnosides. Both recombinant RHM proteins can catalyze the transformation from UDP-d-glucose (UDP-Glc) to UDP-Rha, which was confirmed by LC-MS and formation of flavonol rhamnosides. Biochemical analysis showed that both recombinant RHM proteins preferred alkaline conditions in pH range of 8.0-9.0 and had optimal reaction temperature between 25 and 30 °C. PpRHM1 showed the better UDP-Glc substrate affinity with K_m of 360.01 μM. Gene expression analysis showed different transcript levels of both RHMs in all plant tissues tested, indicating the involvement of rhamnosides in various tissues in plant. Such results provide better understanding of UDP-Rha biosynthesis in fruit tree and may be helpful for further investigation of various rhamnose derivatives and their biological functions.

Measuring psychological and physiological stress in emergency clinicians

BACKGROUND

Evidence regarding stress, team structure and decision-making has been used to inform efficacious team composition and deployment. There have been limited attempts to establish the relationship between psychological stress with physiological data within professional environments. The current study explored measures of psychological and physiological stress in Australian emergency practitioners.

METHODS

Thirty-seven staff in an Australian emergency department completed an online survey assessing freedom to make decisions, social support, and psychological job demands. Seven participants provided saliva samples three times daily for seven days (valid n=141 samples). Cortisol levels of the samples were analysed using competitive enzyme immunoassay kits, and α-amylase using kinetic enzyme assay kits.

RESULTS

Years of emergency experience was positively associated with freedom to make decisions, and social support was negatively correlated with psychological demand. No consistent pattern was observed between cortisol level and reported psychological demand, decision freedom or social support. Physical activity was not reflected in elevated α-amylase. Diurnal variation of cortisol and α-amylase was not affected by shiftwork.

CONCLUSIONS

The data supports the case for using multiple assessments to measure stress. While the psychological data is consistent with previous findings, there are possible disparities between psychological reports and physical indicators of stress.

Expression and Characterization of Mammalian Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) are nonheme iron enzymes that catalyze double bond processing of carotenoids and their apocarotenoid metabolites. Mammalian genomes encode three members of this protein family, namely BCO1, BCO2, and RPE65. Mutations and genetic polymorphism in the corresponding genes are associated with inherited blinding diseases, vitamin A deficiency, and high carotenoid plasma levels. Here we describe a method for the heterologous expression of mammalian BCO1 and BCO2 in E. coli and the biochemical characterization of these recombinant enzymes. Dissecting the enzymatic properties of CCDs will advance our knowledge of the biochemical processes that are govern by these disease-associated enzymes and may assist the design of interventions directed against these disease states.

Physiological phenotyping of mammalian cell lines by enzymatic activity fingerprinting of key carbohydrate metabolic enzymes: a pilot and feasibility study

Objective

Enzymatic fingerprinting of key enzymes of glucose metabolism is a valuable analysis tool in cell physiological phenotyping of plant samples. Yet, a similar approach for mammalian cell line samples is missing. In this study, we applied semi-high throughput enzyme activity assays that were originally designed for plant samples and tested their feasibility in extracts of six frequently used mammalian cell lines (Caco2, HaCaT, C2C12, HEK293, HepG2 and INS-1E).

Results

Enzyme activities for aldolase, hexokinase, glucose-6-phosphate dehydrogenase, phosphoglucoisomerase, phosphoglucomutase, phosphofructokinase could be detected in samples of one or more mammalian cell lines. We characterized effects of sample dilution, assay temperature and repeated freeze–thaw cycles causing potential biases. After careful selection of experimental parameters, the presented semi-high throughput methods could be established as useful tool for physiological phenotyping of cultured mammalian cells.

Clinical and pharmaceutical applications of affinity ligands in capillary electrophoresis: A review

Affinity capillary electrophoresis (ACE) is a separation technique that combines a biologically-related binding agent with the separating power and efficiency of capillary electrophoresis. This review will examine several classes of binding agents that have been used in ACE and applications that have been described for the resulting methods in clinical or pharmaceutical analysis. Binding agents that will be considered are antibodies, aptamers, lectins, serum proteins, carbohydrates, and enzymes. This review will also describe the various formats in which each type of binding agent has been used in CE, including both homogeneous and heterogeneous methods. Specific areas of applications that will be considered are CE-based immunoassays, glycoprotein/glycan separations, chiral separations, and biointeraction studies. The general principles and formats of ACE for each of these applications will be examined, along with the potential advantages or limitations of these methods.

DRfit: a Java tool for the analysis of discrete data from multi-well plate assays

Background

Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training.

Results

We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function.

Conclusions

DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2891-5) contains supplementary material, which is available to authorized users.

Performing anaerobic stopped-flow spectrophotometry inside of an anaerobic chamber

The catalytic cycle of most flavin-dependent enzymes can be divided into oxidative and reductive half-reactions. Although some enzymes are oxidized by electron carrier proteins or organic compounds, many use oxygen as the final electron acceptor. In order to properly study the reductive half-reaction of flavin-dependent enzyme that react with oxygen, as in the case of oxidases and monooxygenases, it is necessary to establish anaerobic conditions that will only allow the reduction process to be monitored. The reduced flavoenzyme can be further studied by exposing it to oxygen to monitor the oxidative half-reaction. Anaerobic chambers provide an ideal environment for performing these experiments as they reliably maintain an anaerobic atmosphere inside a large workspace. A common tool used to study flavin-dependent enzymes is the stopped-flow spectrophotometry. This chapter describes methods for performing stopped-flow experiments in an anaerobic chamber. We include information about the chamber components, setting up a stopped-flow spectrophotometer inside of a chamber, preparing anaerobic solutions, and performing experiments to measure the reductive and oxidative half-reactions of flavin-dependent monooxygenases.

Cargo encapsulation in bacterial microcompartments: Methods and analysis

Metabolic engineers seek to produce high-value products from inexpensive starting materials in a sustainable and cost-effective manner by using microbes as cellular factories. However, pathway development and optimization can be arduous tasks, complicated by pathway bottlenecks and toxicity. Pathway organization has emerged as a potential solution to these issues, and the use of protein- or DNA-based scaffolds has successfully increased the production of several industrially relevant compounds. These efforts demonstrate the usefulness of pathway colocalization and spatial organization for metabolic engineering applications. In particular, scaffolding within an enclosed, subcellular compartment shows great promise for pathway optimization, offering benefits such as increased local enzyme and substrate concentrations, sequestration of toxic or volatile intermediates, and alleviation of cofactor and resource competition with the host. Here, we describe the 1,2-propanediol utilization (Pdu) bacterial microcompartment (MCP) as an enclosed scaffold for pathway sequestration and organization. We first describe methods for controlling Pdu MCP formation, expressing and encapsulating heterologous cargo, and tuning cargo loading levels. We further describe assays for analyzing Pdu MCPs and assessing encapsulation levels. These methods will enable the repurposing of MCPs as tunable nanobioreactors for heterologous pathway encapsulation.

Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS)

BACKGROUND

Producing valuable fuels and chemicals from lignin is a key factor for making lignocellulosic biomass economically feasible; however, significant roadblocks exist due to our lack of detailed understanding of how lignin is enzymatically depolymerized and of the range of possible lignin fragments that can be produced. Development of suitable enzymatic assays for characterization of putative lignin active enzymes is an important step towards improving our understanding of the catalytic activities of relevant enzymes. Previously, we have successfully built an assay platform based on glycan substrates containing a charged perfluorinated tag and nanostructure-initiator mass spectrometry to study carbohydrate active enzymes, especially various glycosyl hydrolyses. Here, we extend this approach to develop a reliable and rapid assay to study lignin-modifying enzymes.

RESULTS

Two β-aryl ether bond containing model lignin dimer substrates, designed to be suitable for studying the activities of lignin-modifying enzymes (LMEs) by nanostructure-initiator mass spectrometry (NIMS), were successful synthesized. Small-angle neutron scattering experiments showed that these substrates form micelles in solution. Two LMEs, laccase from the polypore mushroom Trametes versicolor, and manganese peroxidase (MnP) from white rot fungus Nematoloma frowardii, were tested for catalytic activity against the two model substrates. We show that the reaction of laccase and MnP with phenolic substrate yields products that arise from the cleavage of the carbon-carbon single bond between the α-carbon and the adjacent aryl carbon, consistent with the mechanism for producing phenoxy radical as reaction intermediates. Reactions of the nonphenolic substrate with laccase, on the other hand, adopt a different pathway by producing an α-oxidation product; as well as the cleavage of the β-aryl ether bond. No cleavage of the carbon-carbon bond between the α-carbon and the aryl carbon was observed. To facilitate understanding of reaction kinetics, the reaction time course for laccase activity on the phenolic substrate (I) was generated by the simultaneous measurement of all products at different time points of the reaction. Withdrawal of only a small sample aliquot (0.2 μL at each time point) ensured minimum perturbation of the reaction. The time course can help us to understand the enzyme kinetics.

CONCLUSIONS

A new assay procedure has been developed for studying lignin-modifying enzymes by nanostructure-initiator mass spectrometry. Enzyme assays of a laccase and a MnP on phenolic and nonphenolic β-aryl ether substrates revealed different primary reaction pathways due to the availability of the phenoxy radical intermediates. Our assay provides a wealth of information on bond cleavage events not available using conventional colorimetric assays and can easily be carried out in microliter volumes and the quantitative analysis of product formation and kinetics is rapidly achieved by NIMS. This is the first time that NIMS technology was applied to study the activities of lignin-modifying enzymes. Unlike other previous works, our use of amphiphilic guaiacylglycerol β-O-4 substrate (I) enables the formation of micelles. This approach helps avoid the re-polymerization of the resulting monomeric product. As a result, our assay can clearly demonstrate the degradation pathways of phenolic guaiacylglycerol β-O-4 type of molecules with laccase and MnP.

ER Microsome Preparation in Arabidopsis thaliana

Microsomes are vesicles derived from the endoplasmic reticulum (ER) when cells are broken down in the lab. These microsomes are a valuable tool to study a variety of ER functions such as protein and lipid synthesis in vitro.Here we describe a protocol to isolate ER-derived microsomes Arabidopsis thaliana seedlings and exemplify the use of these purified microsomes in enzyme assays with the auxin precursors tryptophan (Trp) or indole-3-pyruvic acid (IPyA) to quantify auxin synthetic capacity in microsomal and cytosolic fractions.

Test of Efficacy of Cellulases for Biomass Degradation

Testing of cellulases on real biomass samples is required to do a true assessment of their efficacy for biomass degradation. Cellulase enzymes belong to a number of different glycosyl hydrolase families, all with different activity, specificity and modes of action. The concerted and synergistic action of these different cellulases determines the efficacy for plant cell wall deconstruction and cellulose hydrolysis. However, the plant cell wall of lignocellulosic materials is a very complex matrix and the efficacy of a cellulase preparation to degrade lignocellulosic materials is influenced by many factors. In this chapter, two protocols for testing efficacy of cellulases on pretreated biomass samples are described. The first protocol describes a small-scale setup employing low solids concentration that easily enables the testing of a larger number of samples. The second protocol describes a method for testing the efficacy of cellulases at conditions more closely resembling industrial conditions, i.e., high solids concentrations. Both protocols can be used to test the cellulases under a variety of substrate types, substrate concentrations, enzyme loadings and process conditions. The protocols can also be used to evaluate different feedstocks.

Characterization of Substrate, Cosubstrate, and Product Isotope Effects Associated With Enzymatic Oxygenations of Organic Compounds Based on Compound-Specific Isotope Analysis

Enzymatic oxygenations are among the most important biodegradation and detoxification reactions of organic pollutants. In the environment, however, such natural attenuation processes are extremely difficult to monitor. Changes of stable isotope ratios of aromatic pollutants at natural isotopic abundances serve as proxies for isotope effects associated with oxygenation reactions. Such isotope fractionations offer new avenues for revealing the pathway and extent of pollutant transformation and provide new insights into the mechanisms of catalysis by Rieske non-heme ferrous iron oxygenases. Based on compound-specific C, H, N, and O isotope analysis, we present a comprehensive methodology with which isotope effects can be derived from the isotope fractionation measured in substrates, the cosubstrate O₂, and organic oxygenation products. We use dioxygenation of nitrobenzene and 2-nitrotoluene by nitrobenzene dioxygenase as illustrative examples to introduce different mathematical procedures for deriving apparent substrate and product isotope effects. We present two experimental approaches to control reactant and product turnover for isotope fractionation analysis in experimental systems containing purified enzymes, E. coli clones, and pure strains of environmental microorganisms. Finally, we present instrumental procedures and sample treatment instructions for analysis of C, H, and N isotope analysis in organic compounds and O isotope analysis in aqueous O₂ by gas and liquid chromatography coupled to isotope ratio mass spectrometry.

Isolation and characterization of bioactive metabolites producing marine Streptomyces parvulus strain sankarensis-A10

The significance and frequency of marine microorganisms as producers of bioactive metabolites-a natural source of drug discovery had varied significantly during the last decades, making marine ecosystem a huge treasure trove of novel isolates and novel compounds. Among the twelve actinomycetes isolated from marine sediment sample (Lat. 17°41'962″N, Long. 83°19'633″E), amylase, protease, lipase and cellulase activities were exhibited by 8,7,4,3 isolates respectively. Five isolates exhibited l-asparaginase activity, while 5, 6, 2 isolates exhibited antibacterial, antifungal and antimicrobial activities respectively. One isolate VMS-A10 efficiently producing alpha-amylase (25.53 ± 0.50 U/mL), protease (19.26 ± 0.25 U/mL), lipase (36.25 ± 0.10 U/mL), cellulase (14.43 ± 0.513 U/mL), l-asparaginase (0.125 ± 0.004 U/mL), antimicrobial metabolites against B. subtilis (503.33 ± 5.77 U/mL), S. aureus (536.66 ± 5.77 U/mL), E. coli (533.33 ± 5.77 U/mL), P. aeruginosa (500.00 ± 10.0 U/mL), MRSA (538.33 ± 5.77 U/mL), C. albicans (353.33 ± 11.54 U/mL) and A. niger (443.33 ± 15.27 U/mL) was selected, identified on the basis of morphological, cultural, physiological, and biochemical properties together with 16S rDNA sequence, designated as Streptomyces parvulus strain sankarensis-A10 and sequencing product (1490 bp) was deposited in the GenBank database under accession number KT906299, Culture Deposit No: NCIM-5601. Isolation and characterization of each potential actinobacteria having immense industrial and therapeutic value on an unprecedented scale from marine sediments of Visakhapatnam coast will have a burgeoning effect.

Acquisition of accurate data from intramolecular quenched fluorescence protease assays

The Intramolecular Quenched Fluorescence (IQF) protease assay utilizes peptide substrates containing donor-quencher pairs that flank the scissile bond. Following protease cleavage, the dequenched donor emission of the product is subsequently measured. Inspection of the IQF literature indicates that rigorous treatment of systematic errors in observed fluorescence arising from inner-filter absorbance (IF) and non-specific intermolecular quenching (NSQ) is incompletely performed. As substrate and product concentrations vary during the time-course of enzyme activity, iterative solution of the kinetic rate equations is, generally, required to obtain the proper time-dependent correction to the initial velocity fluorescence data. Here, we demonstrate that, if the IQF assay is performed under conditions where IF and NSQ are approximately constant during the measurement of initial velocity for a given initial substrate concentration, then a simple correction as a function of initial substrate concentration can be derived and utilized to obtain accurate initial velocity data for analysis.

Electrochemiluminescence bipolar electrode array for the multiplexed detection of glucose, lactate and choline based on a versatile enzymatic approach

A simple, efficient and versatile biosensing platform capable of the multiplexed detection for glucose, lactate and choline was developed by the integration of bipolar electrochemistry and electrochemiluminescence (ECL) imaging. The sensing bipolar electrodes (BPEs) were simply modified via a one-step method adaptable to different enzymes. The biorecognition event happening between the substrate and the corresponding enzyme could be directly reported by the ECL emitted on the same pole from luminol and in situ generated H₂O₂. Under optimized conditions, the BPEs array was successfully applied for the determination of glucose, lactate and choline in the ranges of 0.01-1mM, 0.01-1mM and 0.02-5mM, with the LOD of 7.57μM, 8.25μM and 43.19μM, respectively. Owing to the improved stability of in situ generated H₂O₂, a whole series of analytes testing could be completed in the same BPE biochip. Subsequently, an array chip consisting of nine BPEs enabled the concomitant detection of glucose, lactate and choline, demonstrating the capability for multifunctional detection of biomolecules. This versatile analytical system could be easily extended to sensitive screening in a miniaturized device and point of care testing.

FBZP-16 using the combination of enzyme assays and genome analysis

Identification of bacteria that produce carbohydrolytic enzymes is extremely important given the increased demand for these enzymes in many industries. Twenty lignocellulose-degrading bacterial isolates from Algerian compost and different soils were screened for their potential to produce different enzymes involved in biomass deconstruction. Based on 16S rRNA gene sequencing, the isolates belonged to Proteobacteria and Actinobacteria. Differences among species were reflected both as the presence/absence of enzymes or at the level of enzyme activity. Among the most active species, Bosea sp. FBZP-16 demonstrated cellulolytic activity on both amorphous cellulose (CMC) and complex lignocellulose (wheat straw) and was selected for whole-genomic sequencing. The genome sequencing revealed the presence of a complex enzymatic machinery required for organic matter decomposition. Analysis of the enzyme-encoding genes indicated that multiple genes for endoglucanase, xylanase, β-glucosidase and β-mannosidase are present in the genome with enzyme activities displayed by the bacterium, while other enzymes, such as certain cellobiohydrolases, were not detected at the genomic level. This indicates that a combination of functional screening of bacterial cultures with the use of genome-derived information is important for the prediction of potential enzyme production. These results provide insight into their possible exploitation for the production of fuels and chemicals derived from plant biomass.

Measurement of Enzyme Activities

The determination of enzyme activities in organ or organellar extracts is an important means of investigating metabolic networks and allows testing the success of enzyme-targeted genetic engineering. It also delivers information on intrinsic enzyme parameters such as kinetic properties or impact of effector molecules. This chapter provides protocols on how to assess activities of the enzymes of the core photorespiratory pathway, from 2-phosphoglycolate phosphatase to glycerate 3-kinase.

Fluorescent mannosides serve as acceptor substrates for glycosyltransferase and sugar-1-phosphate transferase activities in Euglena gracilis membranes

Synthetic hexynyl α-D-mannopyranoside and its α-1,6-linked disaccharide counterpart were fluorescently labelled through CuAAC click chemistry with 3-azido-7-hydroxycoumarin. The resulting triazolyl-coumarin adducts, which were amenable to analysis by TLC, HPLC and mass spectrometry, proved to be acceptor substrates for α-1,6-ManT activities in mycobacterial membranes, as well as α- and β-GalT activities in trypanosomal membranes, benchmarking the potential of the fluorescent acceptor approach against earlier radiochemical assays. Following on to explore the glycobiology of the benign protozoan alga Euglena gracilis, α-1,3- and α-1,2-ManT activities were detected in membrane preparations, along with GlcT, Glc-P-T and GlcNAc-P-T activities. These studies serve to demonstrate the potential of readily accessible fluorescent glycans as substrates for exploring carbohydrate active enzymes.

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Assays for the analysis of carbohydrate-active enzymes that rely upon fluorescent acceptor substrates are set out.

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New assays are validated by benchmarking against radiochemical work with known glycosyltransferase activities.

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The installation of a fluorophore on acceptor substrates was easily achieved through click chemistry.

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Fluorescence assays are used to discover GTs activities in Euglena gracilis microsomal membranes.

Synthesis and biological evaluation of santacruzamate A analogues for anti-proliferative and immunomodulatory activity

Santacruzamate A (SCA) is a natural product isolated from a Panamanian marine cyanobacterium, previously reported to have potent and selective histone deacetylase (HDAC) activity. To optimize the enzymatic and cellular activity, 40 SCA analogues were synthesized in a systematic exploration of the zinc-binding group (ZBG), cap terminus, and linker region. Two cap group analogues inhibited proliferation of MCF-7 breast cancer cells, with analogous increased degranulation of cytotoxic T cells (CTLs), while one cap group analogue reduced CTL degranulation, indicative of suppression of the immune response. Additional testing of these analogues resulted in reevaluation of the previously reported SCA mechanism of action. These analogues and the resulting structure-activity relationships will be of interest for future studies on cell proliferation and immune modulation.

In Vitro Activity Assays for MYST Histone Acetyltransferases and Adaptation for High-Throughput Inhibitor Screening

Lysine acetylation is a posttranslational modification that is carried out by acetyltransferases. The MYST proteins form the largest and most diverse family of acetyltransferases, which regulate gene expression, DNA repair, and cell cycle homeostasis, among other activities, by acetylating both histone and nonhistone proteins. This chapter will describe methods for the preparation and biochemical characterization of MYST family acetyltransferases, including protocols for the preparation of recombinant protein, enzyme assays for measuring steady-state parameters, and binding assays to measure cofactor and inhibitor binding. We also provide details on adapting these assays for high-throughput screening for small molecule MYST inhibitors. This chapter seeks to prepare researchers for some hurdles that they may encounter when studying the MYST proteins so that there may be better opportunity to plan appropriate controls and obtain high-quality data.

In Vitro Evaluation of Bacteriocin-Like Inhibitory Substances Produced by Lactic Acid Bacteria Isolated During Traditional Sicilian Cheese Making

Bacteriocins are antimicrobial proteins produced by bacteria that inhibit the growth of other bacteria with a bactericidal or bacteriostatic mode of action. Many lactic acid bacteria (LAB) produce a high diversity of different bacteriocins. Bacteriocinogenic LAB are generally recognised as safe (GRAS) and useful to control the frequent development of pathogens and spoilage microorganisms. For this reason they are commonly used as starter cultures in food fermentations. In this study, the authors describe the results of a screening on 699 LAB isolated from wooden vat surfaces, raw milk and traditional Sicilian cheeses, for the production of bacteriocin-like inhibitory substances, by comparing two alternative methods. The antagonistic activity of LAB and its proteinaceous nature were evaluated using the spot-on-the-lawn and the well-diffusion assay (WDA) and the sensitivity to proteolytic (proteinase K, protease B and trypsin), amylolytic (a-amylase) and lipolytic (lipase) enzymes. The indicator strains used were: Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis. A total of 223 strains (belonging to the species Enterococcus spp., Lactobacillus spp., Pediococcus spp., Streptococcus spp., Leuconostoc spp. and Lactococcus lactis) were found to inhibit the growth of Listeria monocytogenes by using the spot-on-the-lawn method; only 37 of these were confirmed by using the WDA. The direct addition of bacteriocin-producing cultures into dairy products can be a more practical and economic option for the improvement of the safety and quality of the final product.

Need for Methods to Investigate Endocannabinoid Signaling

Endocannabinoids (eCBs) are endogenous lipids able to activate cannabinoid receptors, the primary molecular targets of the cannabis (Cannabis sativa) active principle Δ(9)-tetrahydrocannabinol. During the last 20 years, several N-acylethanolamines and acylesters have been shown to act as eCBs, and a complex array of receptors, metabolic enzymes, and transporters (that altogether form the so-called eCB system) has been shown to finely tune their manifold biological activities. It appears now urgent to develop methods and protocols that allow to assay in a specific and quantitative manner the distinct components of the eCB system, and that can properly localize them within the cell. A brief overview of eCBs and of the proteins that bind, transport, and metabolize these lipids is presented here, in order to put in a better perspective the relevance of methodologies that help to disclose molecular details of eCB signaling in health and disease. Proper methodological approaches form also the basis for a more rationale and effective drug design and therapeutic strategy to combat human disorders.

Analysis of Translesion DNA Synthesis by the Mitochondrial DNA Polymerase γ

Mitochondrial DNA is replicated by the nuclear-encoded DNA polymerase γ (pol γ) which is composed of a single 140 kDa catalytic subunit and a dimeric 55 kDa accessory subunit. Mitochondrial DNA is vulnerable to various forms of damage, including several types of oxidative lesions, UV-induced photoproducts, chemical adducts from environmental sources, as well as alkylation and inter-strand cross-links from chemotherapy agents. Although many of these lesions block DNA replication, pol γ can bypass some lesions by nucleotide incorporation opposite a template lesion and further extension of the DNA primer past the lesion. This process of translesion synthesis (TLS) by pol γ can occur in either an error-free or an error-prone manner. Assessment of TLS requires extensive analysis of oligonucleotide substrates and replication products by denaturing polyacrylamide sequencing gels. This chapter presents protocols for the analysis of translesion DNA synthesis.

Inhibitors of Ceramidases

The topic of ceramidases has experienced an enormous boost during the last few years. Ceramidases catalyze the degradation of ceramide to sphingosine and fatty acids. Ceramide is not only the central hub of sphingolipid biosynthesis and degradation, it is also a key molecule in sphingolipid signaling, promoting differentiation or apoptosis. Acid ceramidase inhibition sensitizes certain types of cancer to chemo- and radio-therapy and this is suggestive of a role of acid ceramidase inhibitors as chemo-sensitizers which can act synergistically with chemo-therapeutic drugs. In this review, we summarize the development of ceramide analogues as first-generation ceramidase inhibitors together with data on their activity in cells and disease models. Furthermore, we describe the recent developments that have led to highly potent second-generation ceramidase inhibitors that act at nanomolar concentrations. In the third part, various assays of ceramidases are described and their relevance for accurately measuring ceramidase activities and for the development of novel inhibitors is highlighted. Besides potential clinical implications, the recent improvements in ceramidase inhibition and assaying may help to better understand the mechanisms of ceramide biology.

Applicability of fluorescence-based sensors to the determination of kinetic parameters for O₂ in oxygenases

Optical methods for O2 determination based on dynamic fluorescence quenching have been applied to measure oxygen uptake rates in cell culture and to determine intracellular oxygen levels. Here we demonstrate the applicability of fluorescence-based probes in determining kinetic parameters for O2 using as an example catalysis by a cofactor-independent oxygenase (DpgC). Fluorescence-based sensors provide a direct assessment of enzyme-catalyzed O2 consumption using commercially available, low-cost instrumentation that is easily customizable and, thus, constitutes a convenient alternative to the widely used Clark-type electrode, especially in cases where chemical interference is expected to be problematic.

Micro-organic pollutants and biological response of mussels in marinas and ship building/breaking yards in Turkey

Concentrations of PAHs, PCBs and OCPs in sediments and mussels (caged and/or native) were determined at 16 stations in six major sites of coastal Turkey. The biological effects of pollution were evaluated using sediment toxicity tests and enzyme activity assays. EROD, PROD, GST, AChE, CaE, and GR activities were evaluated using the digestive glands of mussels. The total PAH concentrations in the sediments varied between nd and 79,674 ng g(-1) dw, while the total OCP concentrations were in the range of nd to 53.7 ng g(-1) dw. The total PAH concentrations in mussels varied between 22.3 and 37.4 ng g(-1) ww. The average concentrations of total PCBs in mussels were 2795 pg g(-1) ww in the shipyard, 797 pg g(-1) ww in Marina 2 and 53 pg g(-1) ww in Marina 1 stations. The results of whole-sediment toxicity tests showed a strong correlation between toxicity test results and pollutant concentrations. Selected cytosolic enzyme activities in digestive glands differed significantly depending on localities. These differences in enzyme activities were mainly related to the different pollutant levels of the sampling sites. The micro-organic contaminant profile patterns, toxicity tests and biomarker studies showed that shipyards and shipbreaking yards are the major potential sources of organic pollution in coastal areas.

A case of mucolipidosis II presenting with prenatal skeletal dysplasia and severe secondary hyperparathyroidism at birth

Mucolipidosis II (ML II) or inclusion cell disease (I-cell disease) is a rarely occurring autosomal recessive lysosomal enzyme-targeting disease. This disease is usually found to occur in individuals aged between 6 and 12 months, with a clinical phenotype resembling that of Hurler syndrome and radiological findings resembling those of dysostosis multiplex. However, we encountered a rare case of an infant with ML II who presented with prenatal skeletal dysplasia and typical clinical features of severe secondary hyperparathyroidism at birth. A female infant was born at 37⁺¹ weeks of gestation with a birth weight of 1,690 g (<3rd percentile). Prenatal ultrasonographic findings revealed intrauterine growth retardation and skeletal dysplasia. At birth, the patient had characteristic features of ML II, and skeletal radiographs revealed dysostosis multiplex, similar to rickets. In addition, the patient had high levels of alkaline phosphatase and parathyroid hormone, consistent with severe secondary neonatal hyperparathyroidism. The activities of β-D-hexosaminidase and α-N-acetylglucosaminidase were moderately decreased in the leukocytes but were 5- to 10-fold higher in the plasma. Examination of a placental biopsy specimen showed foamy vacuolar changes in trophoblasts and syncytiotrophoblasts. The diagnosis of ML II was confirmed via GNPTAB genetic testing, which revealed compound heterozygosity of c.3091C>T (p.Arg1031X) and c.3456_3459dupCAAC (p.Ile1154GlnfsX3), the latter being a novel mutation. The infant was treated with vitamin D supplements but expired because of asphyxia at the age of 2 months.