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A new class of HIV-1 Tat antagonist acting through Tat-TAR inhibition.

The main transcriptional regulator of the human immunodeficiency virus, the Tat protein, recognizes and binds to a small structured RNA element at the 5' end of every viral mRNA, termed TAR. On the basis of published structural data of the molecular interactions between TAR and Tat-related peptides, we defined requirements for potential low-molecular weight inhibitors of TAR recognition by the Tat protein. In accordance with the resulting concept, a series of compounds was synthesized. In vitro evaluation of their potential to directly interfere with Tat-TAR interaction was used to define a new chemical class of potent Tat antagonistic substances. The most active compound competed with Tat-TAR complexation with a competition dose CD50 of 22 nM in vitro and blocked HIV expression in a cellular Tat transactivation system with an IC50 of 1.2 microM. The close relation between structural features of the interaction between TAR and a new type of inhibitory agent, "In-PRiNts" (for inhibitor of protein-ribonucleotide sequences), such as CGP 40336A and those of the Tat-TAR complex was confirmed by RNase A footprinting and by two-dimensional NMR. Structural implications for the complex between this class of compounds and TAR RNA will be presented.

Acridines↗

Aminoglycoside-arginine conjugates that bind TAR RNA: synthesis, characterization, and antiviral activity.

Regulation of HIV gene expression is crucially dependent on binding of the trans-activator protein, Tat, to the trans-activation response RNA element, TAR, found at the 5' end of all HIV-1 transcripts. Tat-TAR interaction is mediated by a short arginine-rich domain of the protein. Disruption of this interaction could, in theory, create a state of complete viral latency. A new class of small-molecule peptidomimetic TAR RNA binders, conjugates of aminoglycosides and arginine, was recently designed [Litovchick, A., Evdokimov, A. G., and Lapidot, A. (1999) FEBS Lett. 445, 73-79]. Two of these compounds, the tri-arginine derivative of gentamicin C (R3G) and the tetra-arginine derivative of kanamycin A (R4K), bind efficiently and specifically to TAR RNA. These compounds display negligible toxicity while being transported and accumulated in cell nuclei. Here we present a detailed synthesis and chemical characterization of the aminoglycoside-arginine conjugates R3G and R4K as well as GB4K, the tetra-gamma-guanidinobutyric derivative of kanamycin A. Their binding sites on TAR RNA were assigned by RNase A, uranyl nitrate, and lead acetate footprinting. The conjugates interact with TAR RNA in the widened major groove, formed by the UCU bulge and the neighboring base pairs of the upper stem portion of TAR, the binding site of Tat protein, and Tat-derived peptides (e.g., R52). Our results suggest an additional binding site of R4K and R3G compounds, in the lower stem-bulge region of TAR. The antiviral activity of the conjugates in cultured equine dermal fibroblasts infected with equine infectious anemia virus, used as a model system of HIV-infected cells, is also presented.

Animals↗

Maltose-binding protein interacts simultaneously and asymmetrically with both subunits of the Tar chemoreceptor.

The Tar chemotactic signal transducer of Escherichia coli mediates attractant responses to L-aspartate and to maltose. Aspartate binds across the subunit interface of the periplasmic receptor domain of a Tar homodimer. Maltose, in contrast, first binds to the periplasmic maltose-binding protein (MBP), which in its ligand-stabilized closed form then interacts with Tar. Intragenic complementation was used to determine the MBP-binding site on the Tar dimer. Mutations causing certain substitutions at residues Tyr-143, Asn-145, Gly-147, Tyr-149, and Phe-150 of Tar lead to severe defects in maltose chemotaxis, as do certain mutations affecting residues Arg-73, Met-76, Asp-77, and Ser-83. These two sets of mutations defined two complementation groups when the defective proteins were co-expressed at equal levels from compatible plasmids. We conclude that MBP contacts both subunits of the Tar dimer simultaneously and asymmetrically. Mutations affecting Met-75 could not be complemented, suggesting that this residue is important for association of MBP with each subunit of the Tar dimer. When the residues involved in interaction with MBP were mapped onto the crystal structure of the Tar periplasmic domain, they localized to a groove at the membrane-distal apex of the domain and also extended onto one shoulder of the apical region.

ATP-Binding Cassette Transporters↗

Visualizing tertiary folding of RNA and RNA-protein interactions by a tethered iron chelate: analysis ofHIV-1 Tat-TAR complex.

Replication of human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the trans -activation responsive region (TAR) RNA, a 59 base stem-loop structure located at the 5'-end of all HIV transcripts. We have used an intramolecular RNA self-cleaving strategy to determine the folding of TAR RNA and its interactions with a Tat peptide. We incor-porated an EDTA analog at position 24 in the HIV-1 Tat binding site of the TAR RNA. After isolation and purification of the EDTA-TAR conjugate, RNA self-cleavage was initiated by the addition of an iron salt, ascorbate and hydrogen peroxide. Hydroxyl radicals generated from the tethered Fe(II) cleaved TAR RNA backbone in two localized regions. Sites of RNA cleavage were mapped by sequencing reactions. A Tat fragment, Tat(38-72), specifically inhibited RNA self-cleavage. To determine the structural changes caused by the Tat peptide, we performed Fe(II)-EDTA footprinting experiments on Tat-TAR complex. Our high-resolution footprinting results suggest that the inhibition of self-cleavage of EDTA-TAR is due to two effects of Tat binding: (i) Tat binds in the bulge and protects residues in the vicinity of the bulge from self-cleavage and (ii) RNA goes through a structural change where EDTA-U24 is rigidly positioned out of the helix and cannot get access to other nucleotides in the loop of TAR RNA, which are not protected by the Tat peptide. Our results demonstrate that Fe(II)-EDTA-mediated RNA self-cleavage can be applied to study RNA tertiary structures and RNA-protein interactions.

Binding Sites↗

Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin.

Transcriptional activation by the HIV-1 Tat protein requires specific residues in the hexanucleotide loop and trinucleotide bulge of the TAR RNA stem-loop structure found in the 5'-untranslated leader of all viral transcripts. Tat directly contacts residue U22 in the bulge and is thought to act in concert with cellular factors bound to the loop. We find that HeLa nuclear extracts contain two specific TAR RNA-binding proteins, designated TRP-1 and TRP-2, which compete for binding to the upper portion of the TAR hairpin. Analysis of point mutants in TAR RNA reveals that TRP-1 contacts residues in the loop that are important for trans-activation, whereas TRP-2 contacts the bulge, including the same residue (U22) that is required for the Tat-TAR interaction. Glycerol gradient sedimentation and UV cross-linking experiments indicate that TRP-1 is a large heteromeric complex containing a 185-kD RNA-binding protein, whereas TRP-2 activity derives from a family of 110- to 70-kD proteins. Interestingly, both TRP-1 and TRP-2 promote TAR-dependent transcription in vitro in the presence of Tat, although mixing experiments indicate that each of the three proteins must bind independently to TAR RNA. These findings suggest that the TAR element is recognized by two different nuclear RNA-binding proteins that affect transcriptional regulation by Tat.

Base Sequence↗

Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: organization of the tar region.

The tar locus of Escherichia coli specifies one of the major species of methyl-accepting proteins involved in the chemotactic behavior of this organism. The physical and genetic organization of the tar region was investigated with a series of specialized lambda transducing phages and plasmid clones. The tar gene was mapped at the promoter-proximal end of an operon containing five other chemotaxis-related loci. Four of those genes (cheR, cheB, cheY and cheZ) are required for all chemotactic responses; consequently, polar mutations in the tar gene resulted in a generally nonchemotactic phenotype. The fifth gene, tap, was mapped between the tar and cheR loci and specified the production of a 65-kilodalton methyl-accepting protein. Unlike the tar locus, which is required for chemotaxis to aspartate and maltose, mutants lacking only the tap function had no obvious defects in chemotactic ability. Genetic and physical maps of the tar-tap region were constructed with Mu d1 (Apr lac) insertion mutations, whose polar properties conferred a phenotype suitable for deletion mapping studies. Restriction endonuclease analyses of phage and plasmid clones indicated that all of the genetic coding capacity in the tar region is now accounted for.

Bacterial Proteins↗

Aspartate and maltose-binding protein interact with adjacent sites in the Tar chemotactic signal transducer of Escherichia coli.

The Tar protein of Escherichia coli is a chemotactic signal transducer that spans the cytoplasmic membrane and mediates responses to the attractants aspartate and maltose. Aspartate binds directly to Tar, whereas maltose binds to the periplasmic maltose-binding protein, which then interacts with Tar. The Arg-64, Arg-69, and Arg-73 residues of Tar have previously been shown to be involved in aspartate sensing. When lysine residues are introduced at these positions by site-directed mutagenesis, aspartate taxis is disrupted most by substitution at position 64, and maltose taxis is disrupted most by substitution at position 73. To explore the spatial distribution of ligand recognition sites on Tar further, we performed doped-primer mutagenesis in selected regions of the tar gene. A number of mutations that interfere specifically with aspartate taxis (Asp-), maltose taxis (Mal-), or both were identified. Mutations affecting residues 64 to 73 or 149 to 154 in the periplasmic domain of Tar are associated with an Asp- phenotype, whereas mutations affecting residues 73 to 83 or 141 to 150 are associated with a Mal- phenotype. We conclude that aspartate and maltose-binding protein interact with adjacent and partially overlapping regions in the periplasmic domain of Tar to initiate attractant signalling.

ATP-Binding Cassette Transporters↗

Tar-dependent and -independent pattern formation by Salmonella typhimurium.

When Salmonella typhimurium cells were allowed to swarm on either a minimal or complex semisolid medium, patterns of cell aggregates were formed (depending on the thickness of the medium). No patterns were observed with nonchemotactic mutants. The patterns in a minimal medium were not formed by a mutant in the aspartate receptor for chemotaxis (Tar) or by wild-type cells in the presence of alpha-methyl-D,L-aspartate (an aspartate analog), thus resembling the patterns observed earlier in Escherichia coli (E. O. Budrene and H. C. Berg, Nature [London] 349:630-633, 1991) and S. typhimurium (E. O. Budrene and H. C. Berg, Abstracts of Conference II on Bacterial Locomotion and Signal Transduction, 1993). Distinctively, the patterns in a complex medium had a different morphology and, more importantly, were Tar independent. Furthermore, mutations in any one of the genes encoding the methyl-accepting chemotaxis receptors (tsr, tar, trg, or tcp) did not prevent the pattern formation. Addition of saturating concentrations of the ligands of these receptors to wild-type cells did not prevent the pattern formation as well. A tar tsr tcp triple mutant also formed the patterns. Similar results (no negative effect on pattern formation) were obtained with a ptsI mutant (defective in chemotaxis mediated by the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system [PTS]) and with addition of mannitol (a PTS ligand) to wild-type cells. It therefore appears that at least two different pathways are involved in the patterns formed by S. typhimurium: Tar dependent and Tar independent. Like the Tar-dependent patterns observed by Budrene and Berg, the Tar-independent patterns could be triggered by H(2)O(2), suggesting that both pathways of pattern formation may be triggered by oxidative stress.

Bacterial Proteins↗

TAR loop-dependent human immunodeficiency virus trans activation requires factors encoded on human chromosome 12.

The trans-activator response region (TAR) RNA in the human immunodeficiency virus type 1 (HIV-1) and HIV-2 long terminal repeat forms stem-loop secondary structures in which the loop sequence is essential for trans activation. We investigated how the HIV trans-activation mechanism encoded on human chromosome 12 relates to the TAR RNA loop-dependent pathway. DNA transfection experiments showed that trans activation in human-hamster hybrid cells with the single human chromosome 12 and human T-cell lines was highly dependent on the native sequences of the HIV-1 TAR loop and the HIV-2 5' TAR loop. In nonhuman cell lines or hybrid cells without chromosome 12 that supported trans activation, the cellular mechanism was independent of the HIV-1 TAR loop and the response to mutations in the HIV-2 TAR loops differed from that found in human T-cell lines and human-hamster hybrid cells with chromosome 12. Our results suggest that the human chromosome 12 mechanism interacts directly with the TAR RNA loop or indirectly by regulating TAR RNA-binding proteins.

Animals↗

An intact TAR element and cytoplasmic localization are necessary for efficient packaging of human immunodeficiency virus type 1 genomic RNA.

Although most reports defining the human immunodeficiency virus type 1 (HIV-1) genomic RNA packaging signal have focused on the region downstream of the major 5' splice site, others have suggested that sequences upstream of the splice site may also play an important role. In this study we have directly examined the role played by the HIV-1 TAR region in RNA packaging. For these experiments we used a proviral expression system that is largely independent of Tat for transcriptional activation. This allowed us to create constructs that efficiently expressed RNAs carrying mutations in TAR and to determine the ability of these RNAs to be packaged. Our results indicate that loss of sequences in TAR significantly reduce the ability of a viral RNA to be packaged. The requirement for TAR sequences in RNA packaging was further examined by using a series of missense mutations positioned throughout the entire TAR structure. TAR mutations previously shown to influence Tat transactivation, such as G31U in the upper loop region or UCU to AAG in the bulge (nucleotides [nt] 22 to 24), failed to have any effect on RNA packaging. Mutations which disrupted the portion of the TAR stem immediately below the bulge also had little effect. In contrast, dramatic effects on RNA packaging were observed with constructs containing mutations in the lower portion of the TAR stem. Point mutations which altered nt 5 to 9, 10 to 15, 44 to 49, or 50 to 54 all reduced RNA packaging 11- to 25-fold. However, compensatory double mutations which restored the stem structure were able to restore packaging. These results indicate that an intact lower stem structure, rather than a specific sequence, is required for RNA packaging. Our results also showed that RNA molecules retained within the nucleus cannot be packaged, unless they are transported to the cytoplasm by either Rev/Rev response element or the Mason-Pfizer monkey virus constitutive transport element.

5' Untranslated Regions↗

Anti-TAR polyamide nucleotide analog conjugated with a membrane-permeating peptide inhibits human immunodeficiency virus type 1 production.

The emergence of drug-resistant variants has posed a significant setback against effective antiviral treatment for human immunodeficiency virus (HIV) infections. The choice of a nonmutable region of the viral genome such as the conserved transactivation response element (TAR element) in the 5' long terminal repeat (LTR) may potentially be an effective target for drug development. We have earlier demonstrated that a polyamide nucleotide analog (PNA) targeted to the TAR hairpin element, when transfected into cells, can effectively inhibit Tat-mediated transactivation of HIV type 1 (HIV-1) LTR (T. Mayhood et al., Biochemistry 39:11532-11539, 2000). Here we show that this anti-TAR PNA (PNA(TAR)), upon conjugation with a membrane-permeating peptide vector (transportan) retained its affinity for TAR in vitro similar to the unconjugated analog. The conjugate was efficiently internalized into the cells when added to the culture medium. Examination of the functional efficacy of the PNA(TAR)-transportan conjugate in cell culture using luciferase reporter gene constructs resulted in a significant inhibition of Tat-mediated transactivation of HIV-1 LTR. Furthermore, PNA(TAR)-transportan conjugate substantially inhibited HIV-1 production in chronically HIV-1-infected H9 cells. The mechanism of this inhibition appeared to be regulated at the level of transcription. These results demonstrate the efficacy of PNA(TAR)-transportan as a potential anti-HIV agent.

Anti-HIV Agents↗

Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA.

Replication of human immunodeficiency virus type 1 (HIV-1) is regulated in part through an interaction between the virally encoded trans-activator protein Tat and the trans-activator responsive region (TAR) of the viral RNA genome. Because TAR is highly conserved and its interaction with Tat is required for efficient viral replication, it has received much attention as an antiviral drug target. Here, we report a 2-aminopurine (2-AP) fluorescence-based assay for evaluating potential TAR inhibitors. Through selective incorporation of 2-AP within the bulge (C23 or U24) of a truncated form of the TAR sequence (delta TAR-ap23 and delta TAR-ap24), binding of argininamide, a 24-residue arginine-rich peptide derived from Tat, and Neomycin has been characterized using steady-state fluorescence. Binding of argininamide to the 2-AP deltaTAR constructs results in a four- to 11-fold increase in fluorescence intensity, thus providing a sensitive reporter of that interaction (KD approximately 1 mM). Similarly, binding of the Tat peptide results in an initial 14-fold increase in fluorescence (KD approximately 25 nM), but is then followed by a slight decrease that is attributed to an additional, lower-affinity association(s). Using the deltaTAR-ap23 and TAR-ap24 constructs, two classes of Neomycin binding sites are detected; the first molecule of antibiotic binds as a noncompetitive inhibitor of Tat/argininamide (KD approximately 200 nM), whereas the second, more weakly bound molecule(s) becomes associated in a presumably nonspecific manner (KD approximately 4 microM). Taken together, the results demonstrate that the 2-AP fluorescence-detected binding assays provide accurate and general methods for quantitatively assessing TAR interactions.

2-Aminopurine↗

Discoveries of Tat-TAR interaction inhibitors for HIV-1.

A major problem associated with anti-HIV-1 treatment is rapid emergence of drug-resistant strains. Accordingly, a compelling need is to discover anti-HIV drugs against alternative viral targets in addition to HIV-1 RT, PR, IN and CCR5. One such target is the interaction between HIV Trans-activator of transcription (Tat) protein and Trans Activation Responsive region (TAR) RNA. An arginine-rich motif (ARM) of Tat recognizing both the base sequence and the active conformation of TAR RNA three-base bulge region as well as newly elucidated TAR RNA inactive conformation are important for the specific Tat-TAR interaction. According to the possible binding modes, the inhibitors have been mainly divided into two classes: (1) Compounds binding directly to TAR RNA either to the TAR RNA three-base bulge region alone or to the three-base bulge together with the lower and upper-stem/Loop region. (2) Compounds binding directly to Tat protein with high affinity, thus potently inhibiting HIV-1. They both block Tat trans-activation in the formation of the Tat/TAR complex to exert antiviral activity in primary human cells. Recent researches also focus on the drugs targeting specificity of Tat and TAR by such new assays as capillary electrophoresis and quartz crystal microbalance. Cell-based reporter systems are established for high-throughput screening of novel compounds that interfere with Tat transactivation. The identification of dominant-negative mutants also finds wide application in this field. The Tat-TAR interaction is an important target in efforts to develop anti-HIV gene therapy or potential therapeutic antiviral agents for the treatment of HIV-1 infections.

Amides↗

Inhibition of HIV-1 in CEM cells by a potent TAR decoy.

TAR decoys are short RNA oligonucleotides, corresponding to the HIV TAR sequence, which inhibit HIV expression and replication by blocking the binding of the HIV regulatory protein Tat to the authentic TAR region. In previous studies, TAR decoys expressed from a tRNA polIII promoter were moderately effective at inhibiting HIV in isolated human T cell lines and less effective at inhibiting HIV in peripheral blood CD4+ T cells. In this study, a series of modifications was introduced into the tRNA expression cassette in order to improve their effectiveness. These modifications included the addition of sequences which are predicted to have stem-loop secondary structures and addition of a wild-type tRNA processing site. TAR decoy RNA expressed in CEM cells from modified tRNA-based expression cassettes yielded five- to 20-fold more TAR transcripts than unmodified tRNA-based expression cassettes. HIV replication, as measured by a flow cytometric method to quantify intracellular viral p24 expression, was significantly reduced in polyclonal populations of CEM cells expressing a modified tRNA-TAR transcript that contains a wild-type tRNA processing site and stem-loops 5' and 3' to the TAR sequence. Similar modifications to the tRNA expression cassette also increased the intracellular concentration of a random test oligonucleotide, indicating that this improved expression system may also be useful for antisense and ribozyme based gene inhibition strategies.

Antiviral Agents↗

Nicotine or tar titration in cigarette smoking behavior?

A significant problem in assessing the relative relevance of nicotine and tar yield for compensatory smoking after switching from high to low yield cigarettes is that nicotine and tar yield are highly intercorrelated across conventional cigarettes and that the tar/nicotine ratios vary only within a modest range. A better differentiation between the impacts of nicotine and tar yield was expected by comparing in a laboratory experiment a new low nicotine/medium tar cigarette ("Next") with conventional low nicotine/low tar (ultra-light) cigarettes and with medium nicotine/medium tar cigarettes with respect to nicotine absorption and physiological effects. Twelve females, habitually smoking medium type cigarettes (> or = 0.7 mg nicotine) participated in the study. Neither the number of cigarettes smoked under field conditions nor the puffing behavior during the laboratory experiment differed between the three types of cigarettes. In the laboratory, Next produced only very small increases in plasma nicotine and changes in cardiovascular or EEG measures, whereas the effects of the medium cigarettes were in the expected range and those of the ultra-light cigarettes about halfway in between. The nicotine absorption/nicotine yield and the CO absorption/CO yield ratios were similar for Next and the habitual cigarettes, but about twofold higher for the ultra-light cigarettes. This suggests that gustatory and olfactory sensations, which are supposed to be more dependent on tar than on nicotine yield, may play a greater role for the regulation of smoking behavior than hitherto believed.

Adult↗

Lung cancer risk is proportional to cigarette tar yield: evidence from a prospective study.

The age-adjusted risk for lung cancer among over 120,000 male current cigarette smokers in the American Cancer Society's 1959-1972 prospective study was analyzed according to tar yield and quantity smoked per day. At each quantity level, the risk increased with increasing tar yield, and at each tar level, the risk increased with numbers of cigarettes smoked daily. The risks in smokers of cigarettes with the lowest yields, however, far exceeded those of former smokers and nonsmokers. The excess lung cancer risk for current smokers was directly proportional to the estimated total milligrams of tar consumed daily: SMR = 100 + 1.731 x milligrams tar per day. Tar yields today are much lower than they were at the time of this study and presage an eventual reduction (but not elimination) of lung cancer risk for those who continue to smoke cigarettes, especially among lifetime smokers of low-tar cigarettes.

Humans↗

Assessment of the multi-compound non-equilibrium dissolution behaviour of a coal tar containing PAHs and phenols into water.

Herein, an experimental study coupled with a model in order to assess the non-equilibrium and multi-compound dissolution behaviour of a coal tar containing PAHs and phenols into water, is presented. For this aim, two experimental studies has been carried out: (1) coal tar-water partition equilibrium and (2) dissolution dynamics of coal tar under controlled hydrodynamic conditions in percolation columns packed with glass beads. The dissolution amount of the three target constituents (i.e. phenol, naphthalene and phenanthrene) was monitored by UV detection. The dissolution behaviour was modelled using a predictive fraction approach. The partition coefficients have been estimated from experimental data and the obtained results show that the partition coefficient of each constituent between the aqueous phase and the tar depends on the activities of the constituent in both phases and cannot be estimated only from the solubility of the pure compound in water. The non-equilibrium dissolution model was established, applied for the experimental conditions and validated for three target compounds adjusting the effective interfacial area between tar and water. This parameter is specific of the experimental set-up. The global behaviour of coal tar has been modelled taking into account four categories of compounds according to their water solubility and volatilities. The mass transfer parameters have been estimated using available correlations. The results of this paper indicate that a model based on component fractions can be used to assess the non-equilibrium dissolution behaviour of a coal tar.

Coal Tar↗

Study of the composition of tars produced from blends of coal and polyethylene wastes using high-performance liquid chromatography.

Tars produced at semi-industrial scale in a coke oven of 6 x 10(3) kg capacity were used to investigate the effect of using polyethylene waste as an additive in the carbonization process with coal. The polyethylene wastes used were low-density polyethylene from the agriculture greenhouses and high-density polyethylene from domestic sources. The high-performance liquid chromatography analysis of the soluble fractions in toluene and carbon disulfide, using two polystyrene-divinylbenzene columns and a mixture of dichloromethane-methanol as a mobile phase, provides useful information on the composition of tars and their derived pitches in terms of the substitution and molecular topology of polynuclear aromatic compounds (PACs). Differences in composition of tars produced with polyethylene waste at 1% (w/w) have been found to be negligible, while a higher amount of the waste (3%, w/w) promoted the formation of peri-condensed PACs at the expense of the substituted cata-condensed PACs. This behaviour is due to more extensive secondary reactions of tar precursors via dealkylation and aromatic condensation taking place during the carbonization process as a consequence of a more viscous co-carbonizing system. Changes in tar composition caused by this amount of polyethylene waste addition were comparable to those promoted by an increase in the carbonization temperature at semi-industrial and industrial ovens and by the coal preheating before the carbonization process. The characteristic features in tar composition were also found for the derived pitches from tars obtained with the polyethylene waste addition.

Chromatography, High Pressure Liquid↗