Estimating the Risk of Chronic Pain: Development and Validation of a Prognostic Model (PICKUP) for Patients with Acute Low Back Pain

BackgroundLow back pain (LBP) is a major health problem. Globally it is responsible for the most years lived with disability. The most problematic type of LBP is chronic LBP (pain lasting longer than 3 mo); it has a poor prognosis and is costly, and interventions are only moderately effective. Targeting interventions according to risk profile is a promising approach to prevent the onset of chronic LBP. Developing accurate prognostic models is the first step. No validated prognostic models are available to accurately predict the onset of chronic LBP. The primary aim of this study was to develop and validate a prognostic model to estimate the risk of chronic LBP.ConclusionsBased on its performance in these cohorts, this five-item prognostic model for patients with acute LBP may be a useful tool for estimating risk of chronic LBP. Further validation is required to determine whether screening with this model leads to a net reduction in unnecessary interventions provided to low-risk patients.     

Regulation of DNA metabolic enzymes upon induction of preB cell development and V(D)J recombination: up-regulation of DNA polymerase delta.

Withdrawal of interleukin-7 from cultured murine preB lymphocytes induces cell differentiation including V(D)J immunoglobulin gene rearrangements and cell cycle arrest. Advanced steps of the V(D)J recombination reaction involve processing of coding ends by several largely unidentified DNA metabolic enzymes. We have analyzed expression and activity of DNA polymerases alpha, beta, delta and epsilon, proliferating cell nuclear antigen (PCNA), topoisomerases I and II, terminal deoxynucleotidyl transferase (TdT) and DNA ligases I, III and IV upon induction of preB cell differentiation. Despite the immediate arrest of cell proliferation, DNA polymerase delta protein levels remained unchanged for approximately 2 days and its activity was up-regulated several-fold, while PCNA was continuously present. Activity of DNA polymerases alpha,beta and epsilon decreased. Expression and activity of DNA ligase I were drastically reduced, while those of DNA ligases III and IV remained virtually constant. No changes in DNA topoisomerases I or II expression and activity occurred and TdT expression was moderately increased early after induction. Our results render DNA polymerase delta a likely candidate acting in DNA synthesis related to V(D)J recombination in lymphocytes.     

The Family X DNA Polymerase from Deinococcus radiodurans Adopts a Non-standard Extended Conformation

Deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded DNA breaks. One of the players in this pathway is an X family DNA polymerase (PolX_Dr). Deletion of PolX_Dr has been shown to decrease the rate of repair of double-stranded DNA breaks and increase cell sensitivity to gamma-rays. A 3′→5′ exonuclease activity that stops cutting close to DNA loops has also been demonstrated. The present crystal structure of PolX_Dr solved at 2.46-Å resolution reveals that PolX_Dr has a novel extended conformation in stark contrast to the closed “right hand” conformation commonly observed for DNA polymerases. This extended conformation is stabilized by the C-terminal PHP domain, whose putative nuclease active site is obstructed by its interaction with the polymerase domain. The overall conformation and the presence of non standard residues in the active site of the polymerase X domain makes PolX_Dr the founding member of a novel class of polymerases involved in DNA repair but whose detailed mode of action still remains enigmatic.DNA replication and repair are functions that are of vital importance for the maintenance of cellular life. These functions are carried out by various DNA replicating engines, most of them acting as multiprotein complexes. Deinococcus radiodurans, a Gram-positive bacterium, is characterized by an extraordinary resistance to ionizing radiation and desiccation. After radiation induced cutting of its 3.28-megabase genome into hundreds of small fragments, it is capable of reassembling it completely (1). Different hypotheses have been suggested to explain this radioresistance. A recently proposed mechanism involves the creation of long linear DNA intermediates by an extended synthesis-dependent strand annealing process, where overlapping chromosomal fragments are used both as primers and as templates for synthesis of complementary single strands (2). Recircularization of chromosomes would be assured by homologous recombination. Although DNA polymerase I is one of the main enzymes involved in this process, it was shown that other proteins affect double strand break repair efficiency in D. radiodurans. One of these is an X family DNA polymerase (PolX_Dr)⁵ (3). Cells devoid of PolX_Dr protein show increased sensitivity to γ-irradiation and a longer delay in the restoration of an intact genome after irradiation. It was therefore proposed that PolX_Dr has an important role in double strand break repair in D. radiodurans. The contribution of PolX_Dr may become essential for instance when damage gets too important or, alternatively, it may act in different repair pathways from polymerase I. Indeed, some of the X DNA polymerases, such as Saccharomyces cerevisiae Pol4 and human polymerase λ (4) have been proposed to play important roles in different DNA repair processes, including non-homologous end-joining (5). It was shown that PolX_Dr also has strong 3′→5′ exonuclease activity that is stimulated by Mn²⁺ (6). This activity is associated with proofreading mechanisms in other polymerase families and encoded by protein domains or subunits distinct from the polymerase catalytic domain (7). Curiously the exonuclease activity of PolX_Dr is modulated upon encounter of a stem-loop structure. The combination of both activities leads to the hypothesis that PolX_Dr might be involved in DNA repair, potentially non-homologous end-joining, by processing damaged DNA or repair intermediates, thus generating substrates for other repair proteins (6). Very recently an orthologue of PolX from Bacillus subtilis was characterized. It was shown that PolX_Bs is a template-directed DNA polymerase acting on DNA gaps with a downstream 5′ phosphate group, suggesting it may play a role in base excision repair (8).DNA polymerases all combine a catalytic palm domain, a thumb domain, binding double-stranded DNA, and a finger domain that fixes the incoming nucleotide. The polymerase domain of the X family belongs to the Polβ-like nucleotidyltransferase superfamily, sharing ∼25% amino acid identity with the DNA polymerase domains of Polλ, Pol4, and Polβ. PolX_Dr has a second domain at the C terminus called PHP, with strong sequence identity with the histidinol phosphatase involved in histidine transport in bacteria. Due to its similarity to histidinol phosphatase and the presence of a trinuclear zinc site, the PolX_Dr PHP domain is thought to function as phosphoesterase (9). In the context of DNA polymerases, this activity might be responsible for the degradation of pyrophosphate, thus driving the polymerization reaction, or contributes to a nuclease reaction that would be involved in proofreading the newly synthesized strand. The deletion of the PHP domain also had a negative effect on survival of γ-irradiated cells suggesting that this domain possesses a function in DNA repair. Unexpectedly, deletion of the PHP domain destroys structure modulated but not the general 3′→5′ exonuclease activity (6). No activity could be demonstrated for the PHP domain alone.In this report we present the crystal structure of PolX_Dr at 2.46-Å resolution. Surprisingly, PolX_Dr adopts a stretched out conformation instead of the commonly observed closed right hand conformation. In the active site of the polymerase catalytic domain, the two universally conserved aspartates are replaced by two glutamates, whereas the active site of the PHP domain is obstructed by its interaction with the polymerase domain.     

The dnaZ protein, the gamma subunit of DNA polymerase III holoenzyme of Escherichia coli

The dnaZ protein has been purified to near-homogeneity using an in vitro complementation assay that measures the restoration of activity in a crude enzyme fraction from the dnaZ mutant deficient in the replication of phi X174 DNA. Over 70-fold overproduction of the protein was obtained with a bacteriophage lambda lysogen carrying the dnaZ gene. The purified protein, under reducing and denaturing conditions, has a molecular weight of 52,000 and appears to be a dimer in its native form. The dnaZ protein is judged to be th 52,000-dalton gamma subunit of DNA polymerase III holoenzyme (McHenry, C., and Kornberg, A. (1977) J. Biol. Chem. 252, 6478-6484) for the following reasons: (i) highly purified DNA polymerase III holoenzyme contains a 52,000-dalton polypeptide and has dnaZ-complementing activity; (ii) the 52,000-dalton polypeptide is associated tightly with the DNA polymerase III holoenzyme and can be separated from the DNA polymerase III core only with severe measures; (iii) no other purified replication protein, among 14 tested, contains dnaZ protein activity; and (iv) the abundance of dnaZ protein, estimated at about 10 dimer molecules per Escherichia coli cell, is similar to that of the DNA polymerase III core. Among several circular templates tested in vitro (i.e. single stranded phi X174, G4 and M13 DNAs, and duplex phi X174 DNA), all rely on dnaZ protein for elongation by DNA polymerase III holoenzyme. The protein acts catalytically at a stoichiometry of one dimer per template.     

Glucose metabolism in the mucosa of the small intestine. A study of hexokinase activity

1. The intracellular distribution of hexokinase activity was studied in the mucosa of rat and guinea-pig small intestine. In the rat 60% and in the guinea pig 45% of the hexokinase activity of homogenates were recovered in a total particulate fraction that contained only 5-17% of the homogenate activity of hexose phosphate isomerase, pyruvate kinase, lactate dehydrogenase and overall glycolysis (formation of lactate from glucose). 2. Fractionation of homogenates from guineapig small intestine showed that the particulate hexokinase activity was chiefly in the mitochondrial fraction with a small proportion in the nuclei plus brush-border fraction. 3. After chromatography of the particle-free supernatants on DEAE-cellulose, hexokinase types I and II were determined quantitatively. No evidence was obtained for the presence of hexokinase type III or glucokinase. In the preparations from guinea pigs, hexokinase types I and II amounted to 69% and 31% respectively of the eluted activity; the corresponding values for preparations from rats were 5.8% and 94.2%. 4. Total and specific hexokinase activities decreased significantly in homogenates and particle-free supernatants prepared from the intestinal mucosa of rats starved for 36hr. and increased again after re-feeding. The decrease in hexokinase activity in the particle-free supernatant from starved rats was chiefly due to a decrease in the type II enzyme.     

The effect of starvation on the incorporation of palmitate into glycerides and phospholipids of rat liver homogenates

1. Glyceride biosynthesis from glycerol phosphate and [1-(14)C]palmitate was studied in liver homogenates of rats that were fed ad libitum or starved for 36-40hr. The changes in enzyme activity were related to total DNA content or total liver homogenate as these were found to be equivalent and to be the most meaningful parameters. 2. In liver homogenates from fed rats, labelled palmitate was incorporated mainly into phosphatidate (58% of the total incorporation into lipids), diglycerides (25%) and triglycerides (16%), whereas monoglycerides, cholesterol esters and phospholipids other than phosphatidate were labelled only to a small extent. Addition of particle-free supernatant to full homogenates increased the total incorporation of palmitate by 45% and the pattern of incorporation altered to 53% incorporated into triglycerides, 24% into diglycerides and 17% into phosphatidate. This result suggested that, in liver homogenates, phosphatidate phosphohydrolase (EC 3.1.3.4) may be rate-limiting in the biosynthesis of glycerides via the glycerol phosphate pathway. 3. Upon starvation, the amount of palmitate incorporated per liver into total phospholipids plus glycerides was decreased to between 68% and 75% of that observed with fed animals. In homogenates from fed animals 41-44% of the labelled phospholipids plus glycerides was in glycerides; this value increased to between 63% and 75% with starved rats. Of the palmitate incorporated into total phospholipids, between 85% and 86% was found in phosphatidate, independent of the nutritional state of the animal. The ratio of palmitate incorporated into triglycerides/diglycerides rose from 0.7, obtained with fed rats, to 1.0 with starved animals. 4. These results indicate that starvation caused a decrease in the activity (per total liver) of acyl-CoA-glycerol phosphate acyltransferase(s) (EC 2.3.1.15) and an increase in the activity of acyl-CoA-diglyceride acyltransferase (EC 2.3.1.20). The largest change, however, seemed to be related to the increased activity of the phosphatidate phosphohydrolase in the particle-free supernatant. 5. The latter enzyme was assayed in the particle-free supernatant with membrane-bound phosphatidate as substrate. In starvation, the activity per total liver was increased to between 130% and 190% and the specific activity to between 180% and 320% of the values for fed rats.     

Sites of termination of in vitro DNA synthesis on cis-diamminedichloroplatinum(II) treated single-stranded DNA: a comparison between E. coli DNA polymerase I and eucaryotic DNA polymerases alpha.

We have compared the capacity of the large fragment of E. coli DNA polymerase I and highly purified DNA polymerases alpha from either Drosophila melanogaster embryos or calf thymus to replicate single-stranded M13 mp10 DNA treated with the antitumoral drug cis-diamminedichloroplatinum(II) (cis-DDP). We report that: a) although prokaryotic and eukaryotic enzymes have different structural complexity and dissimilar in vivo functions, their synthesis was blocked in vitro at similar sites on cis-DDP treated DNA; b) this inhibition occurred not only at d(G)n sequences, as previously reported for E. coli DNA polymerase I, (Pinto & Lippard (1985) Proc. Natl. Acad. Sci. USA, 82, 4616-4619) but also at other sequences which may represent putative cis-DDP-DNA adducts.