Suborganellar Localization of Mitochondrial Proteins and Transcripts in Human Cells.

Mitochondria have complex ultrastructure which includes continuous subcompartments, such as matrix, intermembrane space, and two membranes, as well as focal structures, such as nucleoids, RNA granules, and mitoribosomes. Comprehensive studies of the spatial distribution of proteins and RNAs inside the mitochondria are necessary to understand organellar gene expression processes and macromolecule targeting pathways. Here we give examples of distribution analysis of mitochondrial proteins and transcripts by conventional microscopy and the super-resolution technique 3D STORM. We provide detailed protocols and discuss limitations of immunolabeling of mitochondrial proteins and newly synthesized mitochondrial RNAs by bromouridine incorporation and single-molecule RNA FISH in hepatocarcinoma cells.

Numerical Modeling of Groundwater Pollution by Chlorpyrifos, Bromacil and Terbuthylazine. Application to the Buñol-Cheste Aquifer (Spain).

Chlorpyrifos, Bromacil and Terbuthylazine are commonly used as insecticides and herbicides to control weeds and prevent non-desirable growth of algae, fungi and bacteria in many agricultural applications. Despite their highly negative effects on human health, environmental modeling of these pesticides in the vadose zone until they reach groundwater is still not being conducted on a regular basis. This work shows results obtained by version 5.08 of the Pesticide Root Zone Model (PRZM5) numerical model to simulate the fate and transport of Chlorpyrifos, Bromacil and Terbuthylazine between 2006 and 2018 inside the Buñol-Cheste aquifer in Spain. The model uses a whole set of parameters to solve a modified version of the mass transport equation considering the combined effect of advection, dispersion and reactive transport processes. The simulation process was designed for a set of twelve scenarios considering four application doses for each pesticide. Results show that the maximum concentration value for every scenario exceeds the current Spanish Maximum Concentration Limit (0.1 µg/L). Numerical simulations were able to reproduce concentration observations over time despite the limited amount of available data.

Cloning and high-level expression of monomeric human superoxide dismutase 1 (SOD1) and its interaction with pyrimidine analogs.

Superoxide dismutase 1 (SOD1) is known to be involved in the pathogenesis of Amyotrophic Lateral Sclerosis (ALS) and is therefore considered to be an important ALS drug target. Identifying potential drug leads that bind to SOD1 and characterizing their interactions by nuclear magnetic resonance (NMR) spectroscopy is complicated by the fact that SOD1 is a homodimer. Creating a monomeric version of SOD1 could alleviate these issues. A specially designed monomeric form of human superoxide dismutase (T2M4SOD1) was cloned into E. coli and its expression significantly enhanced using a number of novel DNA sequence, leader peptide and growth condition optimizations. Uniformly 15N-labeled T2M4SOD1 was prepared from minimal media using 15NH4Cl as the 15N source. The T2M4SOD1 monomer (both 15N labeled and unlabeled) was correctly folded as confirmed by 1H-NMR spectroscopy and active as confirmed by an in-gel enzymatic assay. To demonstrate the utility of this new SOD1 expression system for NMR-based drug screening, eight pyrimidine compounds were tested for binding to T2M4SOD1 by monitoring changes in their 1H NMR and/or 19F-NMR spectra. Weak binding to 5-fluorouridine (FUrd) was observed via line broadening, but very minimal spectral changes were seen with uridine, 5-bromouridine or trifluridine. On the other hand, 1H-NMR spectra of T2M4SOD1 with uracil or three halogenated derivatives of uracil changed dramatically suggesting that the pyrimidine moiety is the crucial binding component of FUrd. Interestingly, no change in tryptophan 32 (Trp32), the putative receptor for FUrd, was detected in the 15N-NMR spectra of 15N-T2M4SOD1 when mixed with these uracil analogs. Molecular docking and molecular dynamic (MD) studies indicate that interaction with Trp32 of SOD1 is predicted to be weak and that there was hydrogen bonding with the nearby aspartate (Asp96), potentiating the Trp32-uracil interaction. These studies demonstrate that monomeric T2M4SOD1 can be readily used to explore small molecule interactions via NMR.

Visualization of Mitochondrial RNA Granules in Cultured Cells Using 5-Bromouridine Labeling.

The incorporation of nucleoside analogs is a useful tool to study the various functions of DNA and RNA. These analogs can be detected directly by fluorescence or by immunolabeling, allowing to visualize, track, or measure the nucleic acid molecules in which they have been incorporated. In this chapter, methodologies to measure human mitochondrial transcription are described. The nascent RNA that is transcribed from mitochondrial DNA (mtDNA) has been shown to assemble into large ribonucleoprotein complexes that form discrete foci. These structures were called mitochondrial RNA granules (MRGs) and can be observed in vitro by the incorporation of a 5-Bromouridine (BrU), which is subsequently visualized by fluorescent immunolabeling. Here, a combined protocol for the MRGs detection is detailed, consisting of BrU labeling and visualization of one of their bona fide protein components, Fas-activated serine-threonine kinase domain 2 (FASTKD2). Based on immunodetection, the half-life and kinetics of the MRGs under various experimental conditions can further be determined by chasing the BrU pulse with an excess of Uridine.

High-Throughput Measurement of Mitochondrial RNA Turnover in Human Cultured Cells.

RNA turnover is an essential part of the gene expression pathway, and there are several experimental approaches for its determination. High-throughput measurement of global RNA turnover rates can provide valuable information about conditions or proteins that impact gene expression. Here, we present a protocol for mitochondrial RNA turnover analysis which involves metabolic labeling of RNA coupled with quantitative high-throughput fluorescent microscopy. This approach gives an excellent opportunity to discover new factors involved in mitochondrial gene regulation when combined with loss-of-function screening strategy.

Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.

Gene expression is determined by a balance between RNA synthesis and RNA degradation. To elucidate the underlying regulatory mechanisms and principles of this, simultaneous measurements of RNA synthesis and degradation are required. Here, we report the development of "Dyrec-seq," which uses 4-thiouridine and 5-bromouridine to simultaneously quantify RNA synthesis and degradation rates. Dyrec-seq enabled the quantification of RNA synthesis and degradation rates of 4702 genes in HeLa cells. Functional enrichment analysis showed that the RNA synthesis and degradation rates of genes are actually determined by the genes' biological functions. A comparison of theoretical and experimental analyses revealed that the amount of RNA is determined by the ratio of RNA synthesis to degradation rates, whereas the rapidity of responses to external stimuli is determined only by the degradation rate. This study emphasizes that not only RNA synthesis but also RNA degradation is important in shaping gene expression patterns.

In-situ treatment of herbicide-contaminated groundwater-Feasibility study for the cases atrazine and bromacil using two novel nanoremediation-type materials.

Two injectable reactive and sorption-active particle types were evaluated for their applicability in permeable reaction zones for in-situ removal of herbicides ("nanoremediation"). As model substances, atrazine and bromacil were used, two herbicides frequently occurring in groundwater. In order to provide recommendations for best use, particle performance was assessed regarding herbicide degradation and detoxification. For chemical reduction, Carbo-Iron® was studied, a composite material consisting of zerovalent iron and colloidal activated carbon. Carbo-Iron reduced bromacil with increased activity compared to nanoscale zerovalent iron (nZVI). The sole reaction product, 3-sec-butyl-6-methyluracil, showed 500-fold increase in half-maximal-effect concentration (EC50) towards the chlorophyte Scendesmus vacuolatus compared to the parent compound. The detoxification based on dehalogenation confirmed the dependency of the specific mode-of-action on the carbon-halide bond. For atrazine, neither nZVI nor Carbo-Iron showed significant degradation under the conditions applied. As novel subsurface treatment option, Trap-Ox® zeolite FeBEA35 was studied for generation of in-situ permeable oxidation barriers. Both adsorbed atrazine and bromacil underwent fast unselective oxidation. The transformation products of the Fenton-like reaction were identified, and oxidation pathways derived. For atrazine, a 300-fold increase in EC50 for S. vacuolatus was found over the duration of the reaction, and a loss of phytotoxicity to non-detectable levels for bromacil.

A comparison between flow-through cathode and mixed tank cells for the electro-Fenton process with conductive diamond anode.

This work focusses on the production of hydrogen peroxide and in the removal of bromacil by the electro-Fenton process using two different electrochemical cells: mixed tank cell (MTC) and flow-through cell (FTC). Both cells use boron doped diamond (BDD) as anode and carbon felt as cathode to promote the formation of hydrogen peroxide. In the case of the MTC, two surface area ratios, Acathode/Aanode, have been used. Results show that the H2O2 produced by MTC and FTCPSC increases with the time until a stabilization state. For the FTCPSC, the average hydrogen peroxide concentration produced increases progressively with the current, while for MTC the maximum values are found in applying very low current densities. In addition, the FTCPSC provides higher concentrations of hydrogen peroxide for the same current density applied. Regarding the MTC, it can be stated that the higher the area of the cathode, the higher is the amount of H2O2 produced and the lower is the cell voltage (because of a more efficient current lines distribution). The initial oxidation of bromacil is very efficiently attained being rapidly depleted from wastewater. However, the higher production of hydrogen peroxide obtained by the FTCPSC cell does not reflect on a better performance of the electro-Fenton process. Thus, bromacil is better mineralized using the MTC cell with the lowest cathode area. This observation has been explained because larger concentrations of produced hydrogen peroxide seems to benefit the oxidation of intermediates and not the mineralization.

Tolerance and sorption of Bromacil and Paraquat by thermophilic cyanobacteria Leptolyngbya 7M from Costa Rican thermal springs.

We studied the adsorption ability and tolerance of the thermophilic filamentous cyanobacteria Letolyngbya 7M towards Paraquat and Bromacil. Adsorption isotherms at pH = 7.0 showed an adsorption capacity of 24.4 mg/g and 66.8 mg/g, respectively, and a good fit to the Langmuir model (R2 = 0.97 and 0.99, respectively). To evaluate the effect of both herbicides on photosynthetic pigments and viability of cyanobacteria, cell autoflorescence and esterase activity was determined using flow cytometry. Autofluorescence was less sensitive to changes in cell viability, as it was only slightly reduced at high Paraquat and Bromacil concentrations. Herbicide effect on esterase activity is dose-dependent. Bromacil did not cause a significant effect on either chlorophyll a content or cell viability. This study demonstrates the potential of Leptolyngbya 7M to remove Paraquat and Bromacil herbicides from aqueous solution under laboratory conditions.

Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing.

Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.

Probing of G-Quadruplex Structures via Ligand-Sensitized Photochemical Reactions in BrU-Substituted DNA.

We studied photochemical reactions of BrU-substituted G-quadruplex (G4) DNA substrates with two pyrene-substituted polyazamacrocyclic ligands, M-1PY and M-2PY. Both ligands bind to and stabilize G4-DNA structures without altering their folding topology, as demonstrated by FRET-melting experiments, fluorimetric titrations and CD spectroscopy. Notably, the bis-pyrene derivative (M-2PY) behaves as a significantly more affine and selective G4 ligand, compared with its mono-pyrene counterpart (M-1PY) and control compounds. Upon short UVA irradiation (365 nm) both ligands, in particular M-2PY, efficiently sensitize photoreactions at BrU residues incorporated in G4 structures and give rise to two kinds of photoproducts, namely DNA strand cleavage and covalent ligand-DNA photoadducts. Remarkably, the photoinduced strand cleavage is observed exclusively with G4 structures presenting BrU residues in lateral or diagonal loops, but not with parallel G4-DNA structures presenting only propeller loops. In contrast, the formation of fluorescent photoadducts is observed with all BrU-substituted G4-DNA substrates, with M-2PY giving significantly higher yields (up to 27%) than M-1PY. Both ligand-sensitized photoreactions are specific to BrU-modified G4-DNA structures with respect to double-stranded or stem-loop substrates. Thus, ligand-sensitized photoreactions with BrU-substituted G4-DNA may be exploited (i) as a photochemical probe, allowing "photofootprinting" of G4 folding topologies in vitro and (ii) for covalent trapping of G4 structures as photoadducts with pyrene-substituted ligands.

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation.

When steady state RNA levels are compared between two conditions, it is not possible to distinguish whether changes are caused by alterations in production or degradation of RNA. This protocol describes a method for measurement of RNA production, using 5-Bromouridine labelling of RNA followed by immunoprecipitation, which enables investigation of RNA synthesized within a short timeframe (e.g., 1 h). The advantage of 5-Bromouridine-labelling and immunoprecipitation over the use of toxic transcriptional inhibitors, such as α-amanitin and actinomycin D, is that there are no or very low effects on cell viability during short-term use. However, because 5-Bromouridine-immunoprecipitation only captures RNA produced within the short labelling time, slowly produced as well as rapidly degraded RNA can be difficult to measure by this method. The 5-Bromouridine-labelled RNA captured by 5-Bromouridine-immunoprecipitation can be analyzed by reverse transcription, quantitative polymerase chain reaction, and next generation sequencing. All types of RNA can be investigated, and the method is not limited to measuring mRNA as is presented in this example.

5'-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives.

Analysis of RNA stability at genome-wide level is an advanced method in RNA biology that examines the half-life of each transcript. In particular, a pulse-labeling method using uridine analogs enables the determination of half-life of each transcript under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromouridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Applications of high-resolution recycling liquid chromatography: From small to large molecules.

A twin-column recycling separation process (TCRSP) is assembled and used to generate higher speed and/or higher resolution levels than those of the usual non-recycling process at the same back pressure. It enables the users to solve very challenging separation problems caused by too small selectivity factors and/or too low column efficiencies. The relative gain in speed-resolution performance increases with increasing the number of cycles in the TCRSP, decreasing the maximum allowable pressure imposed by the LC system, decreasing the column permeability, and with reducing the separation speed. TCRSP is then particularly attractive for conventional LC systems (5000psi maximum) and columns packed with sub-2µm to 3.5µm particles. The performance of the real TCRSP was compared to that of the ideal TCRSP for which the retention factor is strictly pressure-independent. A broad range of separation problems encountered in conventional non-recycling chromatography can be easily solved by using a TCRSP assembly based on two 15cm long columns. Under adsorption conditions, the TCRSP enables the full baseline separation of polycyclic aromatic hydrocarbon (PAH) isomers (benzo[a]anthracene and chrysene) on a 3.5µm XSelect-HSS T3 phase, the complete or improved resolution of racemic mixtures (4-phenylbutanol and bromacil) using the same 2.5µm cellulose-1 chiral stationary phase, and the full resolution of isotopic compounds (benzene/1,3,5-benzene-d3/benzene-d6) on a 2.7µm Cortecs-C18 phase. Under non-adsorption conditions or in size-exclusion chromatography (SEC), the fractionation of a polystyrene standard mixture (molecular weights of 35, 66, 130, 277, 552, 1210, and 2500kDa) was completed after only 8 cycles on a 1.7µm BEH 200Åphase. Similarly, a mixture of intact proteins with molecular weights of 16.7, 66.4, 150, 660, and 1320kDa was fully resolved on a 2.5µm BEH 450Åphase after only 6 cycles. Finally, TCRSP enables the complete separation of a few high-molecular-weight species (monoclonal antibody aggregates, small relative abundance of 1 for 250) from the intact monomeric monoclonal antibody (Vectibix).

Halogen Bonding in Nucleic Acid Complexes.

Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.

Facile Access to Bromonucleosides Using Sodium Monobromoisocyanurate (SMBI).

Bromonucleosides constitute a significant class of molecules and are well known for their biological activity. 5-Bromouridine, 5-bromo-2'-deoxyuridine, 5-bromouridine-5'-triphosphate, and nucleotides containing 5-bromouridine have been tested and used for numerous biological studies. 8-Bromopurine nucleosides have been used as essential precursors for the synthesis of nucleosides with fluorescent properties. This unit describes protocols for the synthesis of bromonucleosides using sodium monobromoisocyanurate (SMBI) in a straightforward way. Reactions are carried out at room temperature, and aqueous solvent mixtures are used to dissolve the nucleosides. Sodium azide is used as catalyst for the bromination of pyrimidine nucleosides, and no catalyst is necessary for the bromination of purine nucleosides. Unprotected 2'-deoxy pyrimidine and 2'-deoxy purine nucleosides are treated with SMBI to afford C-5 bromo pyrimidine and C-8 bromo purine nucleosides, respectively. This methodology has been found to be efficient for the synthesis of bromonucleosides on gram scale with consistently high yields. © 2017 by John Wiley & Sons, Inc.

Gene length as a biological timer to establish temporal transcriptional regulation.

Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.

Influence of Three Citrus Herbicides on Potential Production of Sorghum bicolor 'Topper 76-6' as a Bioenergy Crop.

Planting bioenergy crops on land previously used for citrus production may offer an alternative source of revenue for growers looking for alternative-to-citrus crops. However, residual herbicides used in citrus production may adversely affect alternative crops. This study evaluated effects of three herbicides (bromacil, norflurazon, and simazine) commonly used in citrus production on the bioenergy crop Sorghum bicolor 'Topper 76-6'. Plants were exposed to herbicides in soil for 1-5 weeks and observations of effects on photosynthetic quantum yield, leaf greenness, height, and biomass were made. Results indicate that concentrations of bromacil and norflurazon greater than 0.09 and 0.07 mg/kg and simazine >0.46 mg/kg will impair growth and development in similar soils. Concentrations below these may also be toxic.

Examining cooperative binding of Sox2 on DC5 regulatory element upon complex formation with Pax6 through excess electron transfer assay.

Functional cooperativity among transcription factors on regulatory genetic elements is pivotal for milestone decision-making in various cellular processes including mammalian development. However, their molecular interaction during the cooperative binding cannot be precisely understood due to lack of efficient tools for the analyses of protein-DNA interaction in the transcription complex. Here, we demonstrate that photoinduced excess electron transfer assay can be used for analysing cooperativity of proteins in transcription complex using cooperative binding of Pax6 to Sox2 on the regulatory DNA element (DC5 enhancer) as an example. In this assay, (Br)U-labelled DC5 was introduced for the efficient detection of transferred electrons from Sox2 and Pax6 to the DNA, and guanine base in the complementary strand was replaced with hypoxanthine (I) to block intra-strand electron transfer at the Sox2-binding site. By examining DNA cleavage occurred as a result of the electron transfer process, from tryptophan residues of Sox2 and Pax6 to DNA after irradiation at 280 nm, we not only confirmed their binding to DNA but also observed their increased occupancy on DC5 with respect to that of Sox2 and Pax6 alone as a result of their cooperative interaction.

Phytotoxicity of chiral herbicide bromacil: Enantioselectivity of photosynthesis in Arabidopsis thaliana.

With the wide application of chiral herbicides and the frequent detection of photosystem II (PSII) herbicides, it is of great importance to assess the direct effects of PSII herbicides on photosynthesis in an enantiomeric level. In the present study, the enantioselective phytotoxicity of bromacil (BRO), typical photosynthesis inhibition herbicide, on Arabidopsis thaliana was investigated. The results showed that S-BRO exhibited a greater inhibition of electron transmission in photosystem I (PSI) of A. thaliana than R-BRO by inhibiting the transcription of fnr 1. S-BRO also changed the chlorophyll fluorescence parameters Y (II), Y (NO), and Y (NPQ) to a greater extent than R-Bro. Transcription of genes psbO2, Lhcb3 and Lhcb6 was down-regulated in an enantioselective rhythm and S-BRO caused more serious influence, indicating that S-BRO did worse damage to the photosystem II (PSII) of A. thaliana than R-BRO. This study suggested that S-BRO disturbed the photosynthesis of plants to a larger extent than R-BRO and provided a new sight to evaluate the phytotoxicity of chiral herbicides.