Labeling 3' Termini of Double-Stranded DNA Using the Klenow Fragment of E. coli DNA Polymerase I.

The Klenow fragment, which retains the template-dependent deoxynucleotide polymerizing activity and the 3' → 5' exonuclease of the holo-enzyme but lacks its powerful 5' → 3' exonuclease activity, is used to fill recessed 3' termini of dsDNA. In this protocol, fragments suitable as templates for the end-filling reaction are produced by digestion of DNA with an appropriate restriction enzyme. The Klenow enzyme is then used to catalyze the attachment of dNTPs to the recessed 3'-hydroxyl groups.

Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers.

This protocol describes the generation of radiolabeled cDNA probes from poly(A)+ RNA in a random priming reaction. Probes of this type are used for differential screening of cDNA libraries.

Measurements of 18 O-Pi uptake indicate fast metabolism of phosphate in tree roots.

Phosphorus (P) nutrition of beech ecosystems depends on soil processes, plant internal P cycling and P acquisition. P uptake of trees in the field is currently not validated due to the lack of an experimental approach applicable in natural forests. Application of radiolabelled tracers such as 33 P and 32 P is limited to special research sites and not allowed in natural environments. Moreover, only one stable isotope of P, namely 31 P, exists. One alternative tool to measure P acquisition in the field could be the use of 18 O-labelled 31 P-phosphate (31 P18 O4 3- ). Phosphate (Pi ) uptake rates calculated from the 18 O enrichment of dried root material after application of 31 Pi 18 O4 3- via nutrient solution was always lower compared to 33 P incorporation, did not show increasing rates of Pi uptake at P deficiency under controlled conditions, and did not reveal seasonal fluctuations in the field. Consequently, a clear correlation between 33 P-based and 18 O-based Pi uptake by roots could not be established. Comparison of Pi  uptake rates achieved from 33 P-Pi and 18 O-Pi application led to the conclusion of high Pi metabolism in roots after Pi uptake. The replacement of 18 O by 16 O from water in 18 O-Pi during root influx, but most probably after Pi uptake into roots, due to metabolic activities, indicates high and fast turnover of Pi . Hence, the use of 18 O-Pi as an alternative tool to estimate Pi acquisition of trees in the field must consider the increase of 18 O abundance in root water that was disregarded in dried root material.

Metabolic Labeling of Protein Antigens with [32P]Orthophosphate.

In this protocol, cells are cultured in the presence of [32P]orthophosphate used by the cell to phosphorylate proteins. Cells must be maintained at 37°C at all times during this procedure. A drop in temperature will significantly reduce cellular metabolic activity and subsequently decrease the uptake of [32P]orthophosphate. Once the cells are labeled, cell lysates are prepared for immunoprecipitation, followed by SDS-PAGE analysis. The gel can be dried directly or transferred onto a nitrocellulose or polyvinylidene fluoride (PVDF) membrane for analysis by western blotting and imaging by autoradiography or phosphorimager.

Relative comparison of tissue specific bioaccumulation and radiation dose estimation in marine and freshwater bivalve molluscs following exposure to phosphorus-32.

With respect to environmental protection, understanding radionuclide bioconcentration is necessary to relate exposure to radiation dose and hence to biological responses. Few studies are available on tissue specific accumulation of short-lived radionuclides in aquatic invertebrates. Short-lived radionuclides such as 32Phosphorus (32P), although occurring in small quantities in the environment, are capable of concentrating in the biota, especially if they are chronically exposed. In this study, we firstly compared tissue specific bioaccumulation and release (depuration) of 32P in adult marine (Mytilus galloprovincialis, MG) and freshwater bivalve molluscs (Dreissena polymorpha, DP). Secondly, using the Environmental Risk from Ionising Contaminants Assessment and Management (ERICA) tool, we calculated tissue specific doses following determination of radionuclide concentration. Marine and freshwater bivalves were exposed for 10 days to varying 32P concentrations to acquire desired whole body average dose rates of 0.10, 1.0 and 10 mGy d-1. Dose rates encompass a screening dose rate value of 10 µGy h-1 (0.24 mGy d-1), in accordance with the ERICA tool. This study is the first to relate tissue specific uptake and release (via excretion) of 32P from two anatomically similar bivalve species. Results showed highly tissue specific accumulation of this radionuclide and similarity of accumulation pattern between the two species. Our data, which highlights preferential 32P accumulation in specific tissues such as digestive gland, demonstrates that in some cases, tissue-specific dose rates may be required to fully evaluate the potential effects of radiation exposure on non-human biota. Differential sensitivity between biological tissues could result in detrimental biological responses at levels presumed to be acceptable when adopting a 'whole-body' approach.

The host plant Pinus pinaster exerts specific effects on phosphate efflux and polyphosphate metabolism of the ectomycorrhizal fungus Hebeloma cylindrosporum: a radiotracer, cytological staining and 31 P NMR spectroscopy study.

Ectomycorrhizal (ECM) association can improve plant phosphorus (P) nutrition. Polyphosphates (polyP) synthesized in distant fungal cells after P uptake may contribute to P supply from the fungus to the host plant if they are hydrolyzed to phosphate in ECM roots then transferred to the host plant when required. In this study, we addressed this hypothesis for the ECM fungus Hebeloma cylindrosporum grown in vitro and incubated without plant or with host (Pinus pinaster) and non-host (Zea mays) plants, using an experimental system simulating the symbiotic interface. We used 32 P labelling to quantify P accumulation and P efflux and in vivo and in vitro nuclear magnetic resonance (NMR) spectroscopy and cytological staining to follow the fate of fungal polyP. Phosphate supply triggered a massive P accumulation as newly synthesized long-chain polyP in H. cylindrosporum if previously grown under P-deficient conditions. P efflux from H. cylindrosporum towards the roots was stimulated by both host and non-host plants. However, the host plant enhanced 32 P release compared with the non-host plant and specifically increased the proportion of short-chain polyP in the interacting mycelia. These results support the existence of specific host plant effects on fungal P metabolism able to provide P in the apoplast of ectomycorrhizal roots.

Quantification and genome-wide mapping of DNA double-strand breaks.

DNA double-strand breaks (DSBs) represent a major threat to the genetic integrity of the cell. Knowing both their genome-wide distribution and number is important for a better assessment of genotoxicity at a molecular level. Available methods may have underestimated the extent of DSBs as they are based on markers specific to those undergoing active repair or may not be adapted for the large diversity of naturally occurring DNA ends. We have established conditions for an efficient first step of DNA nick and gap repair (NGR) allowing specific determination of DSBs by end labeling with terminal transferase. We used DNA extracted from HeLa cells harboring an I-SceI cassette to induce a targeted nick or DSB and demonstrated by immunocapture of 3'-OH that a prior step of NGR allows specific determination of loci-specific or genome wide DSBs. This method can be applied to the global determination of DSBs using radioactive end labeling and can find several applications aimed at understanding the distribution and kinetics of DSBs formation and repair.

Phosphorus uptake, partitioning and redistribution during grain filling in rice.

BACKGROUNDS AND AIMS: In cultivated rice, phosphorus (P) in grains originates from two possible sources, namely exogenous (post-flowering root P uptake from soil) or endogenous (P remobilization from vegetative parts) sources. This study investigates P partitioning and remobilization in rice plants throughout grain filling to resolve contributions of P sources to grain P levels in rice. METHODS: Rice plants (Oryza sativa 'IR64') were grown under P-sufficient or P-deficient conditions in the field and in hydroponics. Post-flowering uptake, partitioning and re-partitioning of P was investigated by quantifying tissue P levels over the grain filling period in the field conditions, and by employing 33P isotope as a tracer in the hydroponic study. KEY RESULTS: Post-flowering P uptake represented 40-70 % of the aerial plant P accumulation at maturity. The panicle was the main P sink in all studies, and the amount of P potentially remobilized from vegetative tissues to the panicle during grain filling was around 20 % of the total aerial P measured at flowering. In hydroponics, less than 20 % of the P tracer taken up at 9 d after flowering (DAF) was found in the above-ground tissues at 14 DAF and half of it was partitioned to the panicle in both P treatments. CONCLUSIONS: The results demonstrate that P uptake from the soil during grain filling is a critical contributor to the P content in grains in irrigated rice. The P tracer study suggests that the mechanism of P loading into grains involves little direct transfer of post-flowering P uptake to the grain but rather substantial mobilization of P that was previously taken up and stored in vegetative tissues.

A practical process for the preparation of [(32)P]S1P and binding assay for S1P receptor ligands.

Sphingosine-1-phosphate receptors (S1PRs) are important regulators of vascular permeability, inflammation, angiogenesis and vascular maturation. Identifying a specific S1PR PET radioligand is imperative, but it is hindered by the complexity and variability of current for binding affinity measurement procedures. Herein, we report a streamlined protocol for radiosynthesis of [(32)P]S1P with good radiochemical yield (36-50%) and high radiochemical purity (>99%). We also report a reproducible procedure for determining the binding affinity for compounds targeting S1PRs in vitro.

3'-End labeling of RNA with yeast Poly(A) polymerase and 3'-deoxyadenosine 5'-[α-32P]triphosphate.

This protocol is used to label RNA molecules (in vitro-synthesized or in vivo-purified RNA molecules) that have free 3'-hydroxyl termini. The reaction is performed in 10 min using yeast poly(A) polymerase and 3'-deoxyadenosine 5'-[α-(32)P]triphosphate (cordycepin 5'-[α-(32)P]triphosphate), a chain-terminating nucleotide. At the end of the procedure, the reaction is desalted by gel filtration to remove any unincorporated nucleotides.

3'-end labeling of RNA with [5'-32P]Cytidine 3',5'-bis(phosphate) and T4 RNA ligase 1.

This protocol is used to radiolabel the 3' ends of RNAs, either synthesized by in vitro transcription or purified from cells or tissues, by ligation of [5'-(32)P]cytidine 3',5'-bis(phosphate) (pCp). [5'-(32)P]pCp can be obtained commercially or prepared in the laboratory using polynucleotide kinase to phosphorylate cytidine-3'-monophosphate (Cp) with [γ-(32)P]ATP. "Homemade" [5'-(32)P]pCp is considerably cheaper and has a higher final concentration than that obtained from commercial sources. The labeling protocol uses T4 RNA ligase 1, which covalently joins [5'-(32)P]pCp to the free 3' hydroxyl of RNA. For best labeling, [5'-(32)P]pCp should be at least equimolar or higher to available 3'-hydroxyl ends. The reaction requires overnight incubation at low temperature. At the end of the procedure, the reaction is desalted by gel filtration to remove any unincorporated [5'-(32)P]pCp.

5'-end labeling of RNA with [γ-32P]ATP and T4 polynucleotide kinase.

This protocol uses T4 polynucleotide kinase to catalyze the transfer of a radiolabeled, terminal (γ) phosphate of ATP to the 5'-hydroxyl terminus of a DNA or RNA molecule. The reaction is very efficient and hence is used as a general method for phosphorylating polynucleotides or oligonucleotides.

Mycorrhizal responses in wheat: shading decreases growth but does not lower the contribution of the fungal phosphate uptake pathway.

Effects have been investigated of reduced C supply (induced by shade) on arbuscular mycorrhizal (AM) colonisation, mycorrhizal growth responses (MGRs) and on AM-mediated and direct uptake of phosphate (Pi) (using (32)P) in wheat, a plant that does not usually respond positively to AM colonisation. Shading markedly reduced growth and shoot/root dry weight ratios of both AM and non-mycorrhizal wheat, indicating decreased photosynthetic C supply. However, shading had very little effect on percent root length colonised by Rhizophagus irregularis or Gigaspora margarita or on MGRs, which remained slightly positive or zero, regardless of shade; there were no growth depressions under shade. By 6 weeks, when the contributions of the AM pathway were measured with (32)P supplied in small hyphal compartments, R. irregularis had supplied 23 to 28% of shoot P with no significant effect of shading. Data show that reduced C availability did not reduce the contribution of the AM pathway to plant P, so the fungi were not acting physiologically as parasites. These results support our previous hypothesis that lack of positive MGR is not necessarily the outcome of excessive C use by the fungi or failure to deliver P via the AM pathway.

Ultraviolet photochemical cross-linking to detect RNA-binding proteins.

RNA is photoreactive on exposure to ultraviolet (UV) light in the 250- to 270-nm range. On UV treatment, RNA bases absorb energy to generate free radicals that can covalently attach to nearby amino acid residues in RNA-bound proteins. UV cross-linking experiments have been extensively used to identify and characterize RNA-binding proteins. The method described here involves the use of (32)P-labeled RNA and crude extracts or purified proteins.

Restriction of virus infection but not catalytic dNTPase activity is regulated by phosphorylation of SAMHD1.

SAMHD1 is a host protein responsible, at least in part, for the inefficient infection of dendritic, myeloid, and resting T cells by HIV-1. Interestingly, HIV-2 and SIVsm viruses are able to counteract SAMHD1 by targeting it for proteasomal degradation using their Vpx proteins. It has been proposed that SAMHD1 is a dGTP-dependent deoxynucleoside triphosphohydrolase (dNTPase) that restricts HIV-1 by reducing cellular dNTP levels to below that required for reverse transcription. However, nothing is known about SAMHD1 posttranslational modifications and their potential role in regulating SAMHD1 function. We used (32)P labeling and immunoblotting with phospho-specific antibodies to identify SAMHD1 as a phosphoprotein. Several amino acids in SAMHD1 were identified to be sites of phosphorylation using direct mass spectrometry. Mutation of these residues to alanine to prevent phosphorylation or to glutamic acid to mimic phosphorylation had no effect on the nuclear localization of SAMHD1 or its sensitivity to Vpx-mediated degradation. Furthermore, neither alanine nor glutamic acid substitutions had a significant effect on SAMHD1 dNTPase activity in an in vitro assay. Interestingly, however, we found that a T592E mutation, mimicking constitutive phosphorylation at a main phosphorylation site, severely affected the ability of SAMHD1 to restrict HIV-1 in a U937 cell-based restriction assay. In contrast, a T592A mutant was still capable of restricting HIV-1. These results indicate that SAMHD1 phosphorylation may be a negative regulator of SAMHD1 restriction activity. This conclusion is supported by our finding that SAMHD1 is hyperphosphorylated in monocytoid THP-1 cells under nonrestrictive conditions.

Analysis of pre-mRNA splicing using HeLa cell nuclear extracts.

This protocol is used to determine the splicing behavior of pre-mRNAs in cell extracts that are capable of carrying out splicing (e.g., nuclear extracts from HeLa cells). (32)P-labeled RNA is incubated under splicing conditions for various times, and the resulting products are analyzed on denaturing polyacrylamide gels.

DNase I footprinting.

DNase I footprinting has found a wide following for both identifying and characterizing DNA-protein interactions, particularly because of its simplicity. The concept is that a partial digestion by DNase I of a uniquely (32)P-end-labeled fragment will generate a ladder of fragments, whose mobilities on a denaturing acrylamide gel and whose positions in a subsequent autoradiograph will represent the distance from the end label to the points of cleavage. Bound protein prevents binding of DNase I in and around its binding site and thus generates a "footprint" in the cleavage ladder. The distance from the end label to the edges of the footprint represents the position of the protein-binding site on the DNA fragment. The position of the binding site can be determined by electrophoresing a DNA sequencing ladder alongside the footprint. DNase I cannot bind directly adjacent to a DNA-bound protein because of steric hindrance. Hence, the footprint gives a broad indication of the binding site, generally 8-10 base pairs (bp) larger than the site itself.

Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments.

The generation of a uniquely (32)P-end-labeled DNA fragment is essential for DNA-binding experiments such as DNase I footprinting and ethylation interference. We describe here a protocol for end-labeling a restriction fragment. For a plasmid DNA bearing a region containing the binding site of interest, cleaving with a single restriction endonuclease generates a 5' overhang containing a phosphate. This is generally necessary for both common forms of fragment end-labeling: phosphorylation with polynucleotide kinase and "filling in the end" with DNA polymerases (e.g., Klenow fragment). For the phosphorylation reaction, as described here, the phosphate is removed with calf intestinal phosphatase or bacterial alkaline phosphatase, and the resulting free 5'-OH is phosphorylated with polynucleotide kinase and [γ-(32)P]ATP. This generates a plasmid labeled at each end with γ-(32)P. The molar amount of plasmid DNA must be below the amount of ATP added to the reaction and the ATP must be of sufficiently high specific activity to generate a fragment labeled to the extent necessary for many DNA-binding experiments. To generate a uniquely end-labeled DNA fragment, the labeled plasmid is heat-treated to inactivate any remaining kinase and recleaved with a second endonuclease, releasing a short DNA fragment and a longer vector fragment. The DNA fragment is purified from the labeled vector on a 5%-8% native polyacrylamide gel. The preparation and labeling of DNA restriction fragments typically takes 1-2 d.

Chlamydia trachomatis transports NAD via the Npt1 ATP/ADP translocase.

Obligate intracellular bacteria comprising the order Chlamydiales lack the ability to synthesize nucleotides de novo and must acquire these essential compounds from the cytosol of the host cell. The environmental protozoan endosymbiont Protochlamydia amoebophila UWE25 encodes five nucleotide transporters with specificities for different nucleotide substrates, including ATP, GTP, CTP, UTP, and NAD. In contrast, the human pathogen Chlamydia trachomatis encodes only two nucleotide transporters, the ATP/ADP translocase C. trachomatis Npt1 (Npt1(Ct)) and the nucleotide uniporter Npt2(Ct), which transports GTP, UTP, CTP, and ATP. The notable absence of a NAD transporter, coupled with the lack of alternative nucleotide transporters on the basis of bioinformatic analysis of multiple C. trachomatis genomes, led us to re-evaluate the previously characterized transport properties of Npt1(Ct). Using [adenylate-(32)P]NAD, we demonstrate that Npt1(Ct) expressed in Escherichia coli enables the transport of NAD with an apparent K(m) and V(max) of 1.7 µM and 5.8 nM mg(-1) h(-1), respectively. The K(m) for NAD transport is comparable to the K(m) for ATP transport of 2.2 µM, as evaluated in this study. Efflux and substrate competition assays demonstrate that NAD is a preferred substrate of Npt1(Ct) compared to ATP. These results suggest that during reductive evolution, the pathogenic chlamydiae lost individual nucleotide transporters, in contrast to their environmental endosymbiont relatives, without compromising their ability to obtain nucleotides from the host cytosol through relaxation of transport specificity. The novel properties of Npt1Ct and its conservation in chlamydiae make it a potential target for the development of antimicrobial compounds and a model for studying the evolution of transport specificity.

The interplay between P uptake pathways in mycorrhizal peas: a combined physiological and gene-silencing approach.

Arbuscular mycorrhizal fungi (AMF) have a key role in plant phosphate (Pi) uptake by their efficient capture of soil phosphorus (P) that is transferred to the plant via Pi transporters in the root cortical cells. The activity of this mycorrhizal Pi uptake pathway is often associated with downregulation of Pi transporter genes in the direct Pi uptake pathway. As the total Pi taken up by the plant is determined by the combined activity of mycorrhizal and direct pathways, it is important to understand the interplay between these, in particular the actual activity of the pathways. To study this interplay we modulated the delivery of Pi via the mycorrhizal pathway in Pisum sativum by two means: (1) Partial downregulation by virus-induced gene silencing of PsPT4, a putative Pi transporter gene in the mycorrhizal pathway. This resulted in decreased fungal development in roots and soil and led to reduced plant Pi uptake. (2) Changing the percentage of AMF-colonized root length by using non-, half-mycorrhizal or full-mycorrhizal split-root systems. The combination of split roots, use of ³²P and ³³P isotopes and partial silencing of PsPT4 enabled us to show that the expression of PsPT1, a putative Pi transporter gene in the direct pathway, was negatively correlated with increasing mycorrhizal uptake capacity of the plant, both locally and systemically. However, transcript changes in PsPT1 were not translated into corresponding, systemic changes in actual direct Pi uptake. Our results suggest that AMF have a limited long-distance impact on the direct pathway.