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Flexibility of BIV TAR-Tat: models of peptide binding.

A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database of three-dimensional structures determined from NMR (1996)) and binding studies of mutants (L. Chen and A. D. Frankel, Proc. Natl. Acad. Sci. USA 92, 5077-5081 (1995)). The lattice and RMSD calculations facilitate the identification of peptide hinge regions that can best utilize the introduction of Gly or other flexible residues. This approach for identifying potential sites amenable to substitution of more flexible residues to enhance peptide binding to RNA targets could be a useful design tool.

Amino Acid Sequence↗

Juniper tar poisoning.

Juniper tar (cade oil) is distilled from the branches and wood of Juniperus oxycedrus. It contains etheric oils, triterpene and phenols, and is used for many purposes in folk medicine. A case is reported of a previously healthy man who ingested a spoonful of home-made extract of Juniperus oxycedrus. The poisoning caused fever, severe hypotension, renal failure, hepatotoxicity, and severe cutaneous burns on the face. After supportive and symptomatic treatment, the patient improved and was discharged in a good condition on the eleventh day.

Adult↗

Fatal keratomas due to deep homografts of the benign papillomas of tarred mouse skin; normal proclivities and neoplastic disabilities as determinants of tumor course.

Six out of eight epidermal papillomas, induced with tar in mice of homogeneous strain, have grown after transfer to the subcutaneous tissue of sucklings and weanlings. Five of them have been thus maintained for nearly or quite a year and a half, and in seven to nine successive groups of mice. The tumor studied longest has been kept going in five parallel lines since its primary implantation. The papillomas have all grown progressively in most instances, and proved fatal. None has altered except through the occurrence of derivative cancers, but these have arisen so often as only to be excluded on transfer by a rigorous selection of grafts. Histologically the papillomas have been of a single, completely unaggressive kind, yet transfer has disclosed great differences in their abilities. The tumors they form are of unique sorts. The cells of some are able-bodied (Type A), capable of spreading along bare connective tissue and keratinizing like normal, reparative epidermis. They line graft pockets, differentiate into the free space these provide, and form cysts densely packed with keratin. The papilloma is thus turned outside in. The cysts become huge as keratin accumulates in them, and eventually they rupture with result either in subcutaneous dissecting cysts or keratinizing surface growths that are often prodigious in size and fantastic in shape, but sometimes are completely like the cutaneous papillomas ordinarily induced by carcinogens, and tend, when small, to regress or come away as these frequently do. One growth of Type A was placed in the peritoneal cavity or in the liver, spleen or lung, and at all these situations it formed introverted cysts resembling the subcutaneous. The cells of other papillomas are more or less crippled (Type C). In extreme instances they are unable to spread laterally, and produce relatively little keratin. They fail to line graft pockets, but their keratin inflames the exposed connective tissue, extravasation ensues, and a continually enlarging, fluid-filled cyst forms, with walls that are bare except where a stalked or cauliflower papilloma exists, projecting inwards. At last the cyst ruptures and a second dissecting cyst forms, also devoid of papilloma tissue; or else the overlying skin undergoes pressure necrosis, the cyst fluid escapes through a rent, and fatal infection ensues. All gradations exist between Type A and Type C. The cancers derivative from both exhibit a marked disability,-though invasive they are almost or quite unable to extend along bare connective tissue. The papillomas that are possessed of this faculty spread beyond them along the cyst wall, and kill the host through their unceasing activity. In collateral work a papilloma was transplanted that was found protruding from the external auditory canal of a mouse which had received an intramuscular injection of methylcholanthrene many months previously. The tumor is now in its 5th generation, after 15 months. The growths it forms are of Type A. All of the papillomas are functioning tumors, with their own cells as the functioning product. Their papilliferous shape, when on the skin, is due solely to inability of their cells to gain space in other ways. Intrinsically they are keratomas. The papillomas do well after transfer to deep situations because the growth of their cells is indirectly promoted, through favoring local conditions. No direct promotion takes place like that when the cells of prostatic and mammary tumors are stimulated to multiply by hormones. Doubtless many agents act in both ways, that is to say by dual promotion.

Allografts↗

Outbreak of necrotizing fasciitis due to Clostridium sordellii among black-tar heroin users.

In California, black tar heroin (BTH) use among injection drug users (IDUs) has resulted in an increased number of cases of wound botulism due to Clostridium botulinum, tetanus due to Clostridium tetani, and necrotizing soft-tissue infections due to a variety of clostridia. From December 1999 to April 2000, nine IDUs in Ventura County, California, developed necrotizing fasciitis; 4 died. Cultures of wound specimens from 6 case patients yielded Clostridium sordellii. Some of the patients appeared to have the toxic shock syndrome previously reported to be characteristic of toxin-mediated C. sordellii infection, which is characterized by hypotension, marked leukocytosis, and hemoconcentration. The suspected source of this outbreak was contaminated BTH that was injected subcutaneously or intramuscularly ("skin popped"). This outbreak of C. sordellii infection serves as another example of how BTH can potentially serve as a vehicle for transmitting severe and often deadly clostridial infections, and reinforces the need to educate IDUs and clinicians about the risks associated with skin popping of BTH.

Adult↗

Genetic analysis of regulatory, promoter, and TAR regions of LTR sequences belonging to HIV type 1 Non-B subtypes.

Transcriptional activation of HIV-1 gene expression is controlled by the interaction of sequence-specific transcription factors with the long terminal repeat (LTR). Information about differences between LTR regions in distinct HIV-1 subtypes is scarce. LTR sequences, including regulatory, enhancer, promoter, and TAR regions, were genetically characterized and compared in 59 HIV-1-infected individuals known to be infected with non-B subtypes. Phylogenetic analyses ascribed the LTR regions to the following subtypes: 10A, 2B, 6C, 1D, 2E, 2F, 16G, 3J, 2H, and 2U. Up to 34% of the samples were LTR/PR recombinants. The LTR region revealed a high degree of genetic variability among distinct HIV-1 subtypes and showed several subtype-specific markers, which hypothetically could influence the interactions with cellular transcription factors, leading to different transcriptional levels among distinct HIV-1 clades. To our knowledge, this is the first characterization of LTR sequences belonging to subtypes J and H.

Adult↗

Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element.

We have extracted from a random population of about 10(9) oligodeoxynucleotides a series of 21-mers that are able to bind to a folded DNA 76-mer used as a template for in vitro transcription of the TAR element of the retrovirus HIV-1, by the T7 RNA polymerase. Five aptastrucs, that is, aptamers able to bind to the structure, out of 15 analyzed sequences, share the consensus motif 5'-PyGGG(TG)PyC, complementary in part to a weak double-stranded region of the target. (The parentheses indicate that either T or G is missing in one of these aptastrucs.) A dissociation constant of about 3 microM was evaluated by electrophoretic mobility shift assay for the winner sequence. Interactions between the aptastruc and the target sequences involve more than Watson-Crick base pairing of the consensus octamer. The binding is chemistry dependent. Phosphorothioate oligodeoxyribonucleotides and 2'-O-methyl oligoribonucleotides derived from the selected aptastrucs exhibit a weak if any affinity for the target.

Base Composition↗

Oncogenic potential of TAR RNA binding protein TRBP and its regulatory interaction with RNA-dependent protein kinase PKR.

TAR RNA binding protein (TRBP) belongs to an RNA binding protein family that includes the double-stranded RNA-activated protein kinase (PKR), Drosophila Staufen and Xenopus xlrbpa. One member of this family, PKR, is a serine/threonine kinase which has anti-viral and anti-proliferative effects. In this study we show that TRBP is a cellular down-regulator of PKR function. Assaying expression from an infectious HIV-1 molecular clone, we found that PKR inhibited viral protein synthesis and that over-expression of TRBP effectively countered this inhibition. In intracellular and in cell-free assays we show that TRBP directly inhibits PKR autophosphorylation through an RNA binding-independent pathway. Biologically, TRBP serves a growth-promoting role; cells that overexpress TRBP exhibit transformed phenotypes. Our results demonstrate the oncogenic potential of TRBP and are consistent with the notion that intracellular PKR function contributes physiologically towards regulating cellular proliferation.

3T3 Cells↗

Expression of the TAR RNA binding protein in human testis.

In testis, several RNA binding proteins have been shown to play a role in the translational regulation of specific transcripts. The human protein TRBP (TAR RNA binding protein) is the homologue of the mouse Prbp (Prm-1 RNA binding protein) involved in the protamine mRNA translational delay. TRBP is known to activate the HIV-1 long terminal repeat but this protein has never been investigated during spermatogenesis. The aim of this work was to analyse the TRBP expression in human testis. By Northern blot analysis, we demonstrated a major 1.5 kb transcript present at a high level in human testis and, to a lesser extent, in some other tissues. In-situ hybridization revealed that this transcript was present only in elongating spermatids. Antibodies raised against a 27 amino acid TRBP-specific peptide revealed a single protein of 43 kDa expressed in the cytoplasm of elongated spermatids. At the ultrastructural level, quantitative analysis of both TRBP mRNA and protein, using electron microscopy in-situ hybridization and immunocytochemistry, showed that TRBP is expressed mainly in spermatids at steps 3-4 of spermiogenesis. These results are in agreement with the probable role of TRBP in the control of human protamine mRNA translation.

Gene Expression↗

Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat--TAR interactions.

RNA-protein complexes isolated following a gel retardation assay can be footprinted within the gel matrix using the chemical nuclease activities of 4,7-dimethyl-, 5,6-dimethyl-, and 3,4,7,8-tetramethyl-1,10-phenanthroline-copper. These complexes are more reactive than 1,10-phenanthroline-copper but share its reaction preference for bulges and loops. The interaction of the coat protein of R-17 with its viral RNA target and tat- and tat-derived peptides with HIV TAR RNA have been studied. In both cases, the RNA sequence opposite a 2-3 nucleotide bulge are protected. Tat-derived peptides inhibit cleavage at sites which intact tat does not protect. These results are consistent with transcription studies which have suggested that truncation of tat increases nonspecific binding.

Amino Acid Sequence↗

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access.

For the binding of peptides to wild-type HIV-1 and BIV TAR RNA and to mutants with bulges of various sizes, changes in the DeltaDelta G values of binding were determined from experimental K d values. The corresponding entropies of these bulges are estimated by enumerating all possible RNA bulge conformations on a lattice and then applying the Boltzmann relationship. Independent calculations of entropies from fluctuations are also carried out using the Gaussian network model (GNM) recently introduced for analyzing folded structures. Strong correlations are seen between the changes in free energy determined for binding and the two different unbound entropy calculations. The fact that the calculated entropy increase with larger bulge size is correlated with the enhanced experimental binding free energy is unusual. This system exhibits a dependence on the entropy of the unbound form that is opposite to usual binding models. Instead of a large initial entropy being unfavorable since it would be reduced upon binding, here the larger entropies actually favor binding. Several interpretations are possible: (i) the higher conformational freedom implies a higher competence for binding with a minimal strain, by suitable selection amongst the set of already accessible conformations; (ii) larger bulge entropies enhance the probability of the specific favorable conformation of the bound state; (iii) the increased freedom of the larger bulges contri-butes more to the bound state than to the unbound state; (iv) indirectly the large entropy of the bound state might have an unfavorable effect on the solvent structure. Nonetheless, this unusual effect is interesting.

Animals↗

Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding.

To quantitatively understand the binding affinity and target selectivity of small-molecule RNA interactions, it is useful to have a rapid, highly reproducible binding assay that can be readily generalized to different RNA targets. To that end, an assay has been developed and validated for measuring the binding of low-molecular weight ligands to RNA by monitoring the fluorescence of a covalently incorporated fluorophore. As a test system, the fluorescence of a pyrene-derivatized HIV-1 TAR (transactivating response element) RNA was measured upon titration with aminoglycoside antibiotics. The binding isotherms thus obtained fit well with a model for a 1:1 interaction and yield an accurate measure of the equilibrium dissociation constant. Among a series of natural aminoglycosides, the binding affinity correlates with the number of amines, supporting an electrostatic compensation model for binding. Furthermore, the ionic strength dependence confirms that much of the binding energy is electrostatic. Finally, by measuring the binding affinity in the presence of nucleic acid competitors, we confirm that although aminoglycosides show high RNA to DNA selectivity, their selectivity among different RNA targets is sub- optimal. We conclude that this newly developed assay can be generalized to measure the binding affinities and selectivities of a variety of small molecules to a specific RNA target.

Aminoglycosides↗

Thrombocytopenia with absent radius (TAR).

Forty examples (27 from the literature and 13 new cases) of a syndrome of hypomegakaryocytic thrombocytopenia with bilateral absence of the radius have been analyzed. This syndrome is designated in this paper as "thrombocytopenia with absent radius (TAR)". The onset of hematologic complications usually occurs at birth or during early infancy. Thrombocytopenia may be episodic and sometimes is accompanied by leukemoid reactions and eosinophilia. Bone marrow examination reveals decreased and/or abnormal megakaryocytes, with normal myeloid and erythroid precursors. Congenital skeletal deformities include bilateral absence of radius, shortening and deformity of the ulnae, and occasionally absence of all the long bones in the arm. The fingers and thumbs are always present. Other skeletal anomalies are frequent. Cardiac anomalies, particularly the tetralogy of Fallot and atrial septal defects, may be present. Other non-skeletal congenital abnormalities are rare. The prognosis is good if the patient survives to one year of age. The syndrome has been compared to Fanconi's anemia, thalidomide embryopathy, limb-cardiovascular syndrome, and a syndrome of multiple congenital malformations, from which it can be distinguished.

Abnormalities, Multiple↗

Candida digboiensis sp. nov., a novel anamorphic yeast species from an acidic tar sludge-contaminated oilfield.

Two strains (TERI-6(T) and TERI-7) of a novel yeast species were isolated from acidic tar sludge-contaminated soil samples collected from Digboi Refinery, Assam, India. These two yeast strains were morphologically, physiologically and phylogenetically identical to each other. No sexual reproduction was observed on corn meal, malt, Gorodkowa, YM or V8 agars. Physiologically, the novel isolates were most closely related to Candida blankii, but differed in eight physiological tests. The prominent differences were the ability of the isolates to assimilate melibiose and inulin and their inability to assimilate d-glucuronate, succinate and citrate. Phylogenetic analysis using the D1/D2 variable domain showed that the closest relative of these strains is C. blankii (2.8 % divergence). Other related species are Zygoascus hellenicus and Candida bituminiphila. The isolates differed from C. blankii by 11 base substitutions in the 18S rRNA gene sequence and by 58 base substitutions in the internal transcribed spacer sequences. The physiological, biochemical and molecular data support the contention that strains TERI-6(T) and TERI-7 represent a novel species, for which the name Candida digboiensis sp. nov. is proposed. The type strain is TERI-6(T) (=MTCC 4371(T)=CBS 9800(T)=JCM 12300(T)).

Candida↗

Clinical manifestations of the thrombocytopenia and absent radii (TAR) syndrome.

Six patients with the classical features of the TAR syndrome were diagnosed at birth. In one case an older sibling was also affected. The characteristic features of foreshortened forearms and radially deviated hands were noted in all cases at presentation and confirmed radiologically. With one exception skeletal abnormalities of the lower limbs were also present. Varying degrees of thrombocytopenia were present at birth with three of the five patients having platelet counts below 50 x 10(9)/L. Bone marrow examination was performed in two patients and revealed an absence of normal megakaryocytes. Two patients with severe thrombocytopenia had bleeding complications during infancy requiring transfusion support. Severe gastroenteritis occurred in two patients, in one of whom it was attributed to cow's milk intolerance. In all patients the platelet count has risen progressively since birth. Orthopedic surgical procedures have been performed without hemorrhagic complications.

Diseases in Twins↗

Wound botulism associated with black tar heroin.

The incidence of wound botulism is increasing and the epidemiology of the disease is changing. The majority of new cases are associated with injection drug use, in particular, the use of Mexican black tar heroin. This case report and discussion of wound botulism illustrate the following important points: Dysphagia, dysphonia, diplopia, and descending paralysis, in association with injection drug use, should alert the treating physician to the possibility of wound botulism. In such patients, the onset of respiratory failure may be sudden and without clinically obvious signs of respiratory weakness. For the reported patient, maximum inspiratory force measurements were the only reliable indicator of respiratory muscle weakness. This is a measurement not routinely performed in the ED, but may prove essential for patients with suspected wound botulism. To minimize the effect of the botulinum toxin and to decrease length of hospital stay, antitoxin administration and surgical wound debridement should be performed early.

Botulism↗

Enhanced biodegradation of phenanthrene in oil tar-contaminated soils supplemented with Phanerochaete chrysosporium.

In recent years, the white rot fungus Phanerochaete chrysosporium has shown promise as an organism suitable for the breakdown of a broad spectrum of environmental pollutants, including polynuclear aromatic hydrocarbons (PAHs). The focus of this study was to determine whether P. chrysosporium could effectively operate in an actual field sample of oil tar-contaminated soil. The soil was loaded with [14C]phenanthrene to serve as a model compound representative of the PAHs. Soil with the native flora present under static, aerobic conditions with buffering (pH 5.0 to 5.5) displayed full mineralization on the order of 20% in 21 days. The addition of P. chrysosporium was synergistic, with full mineralization on the order of 38% in 21 days. In addition to full mineralization, there was an increase in the proportion of radiolabelled polar extractives, both soluble and bound, in the presence of P. chrysosporium. From this study, it is apparent that the native soil microflora can be prompted into full mineralization of PAHs in some contaminated soils and that this mineralization can be enhanced when supplemented with the white rot fungus P. chrysosporium. With further refinement, this system may prove an effective bioremediation technology for soils contaminated with PAHs.

Adsorption↗

Mutationally altered signal output in the Nart (NarX-Tar) hybrid chemoreceptor.

Signal-transducing proteins that span the cytoplasmic membrane transmit information about the environment to the interior of the cell. In bacteria, these signal transducers include sensor kinases, which typically control gene expression via response regulators, and methyl-accepting chemoreceptor proteins, which control flagellar rotation via the CheA kinase and CheY response regulator. We previously reported that a chimeric protein (Nart) that joins the ligand-binding, transmembrane, and linker regions of the NarX sensor kinase to the signaling and adaptation domains of the Tar chemoreceptor elicits a repellent response to nitrate and nitrite. As with NarX, nitrate evokes a stronger response than nitrite. Here we show that mutations targeting a highly conserved sequence (the P box) in the periplasmic domain alter chemoreception by Nart and signaling by NarX similarly. In particular, the G51R substitution converts Nart from a repellent receptor into an attractant receptor for nitrate. Our results underscore the conclusion that the fundamental mechanism of transmembrane signaling is conserved between homodimeric sensor kinases and chemoreceptors. They also highlight the plasticity of the coupling between ligand binding and signal output in these systems.

Bacterial Proteins↗