SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
We report a male child with Thrombocytopenia and Absent Radii (TAR) syndrome but with single absent radius and associated tracheoesophageal fistula which has never been reported till date.
Microbial diversity in four wells along a groundwater flowpath in a coal-tar-waste-contaminated aquifer was examined using RFLP analysis of both 16S rDNA and naphthalene dioxygenase (NDO) genes. Amplified ribosomal DNA restriction analysis (ARDRA) relied upon eubacteria-specific primers to generate four clone libraries. From each library, 100 clones were randomly picked for analysis. Sixty percent of 400 clones contained unique ARDRA patterns. Diversity indices calculated for each community were high (Shannon-Weaver, H = 3.53 to 3.69). Clones representing ARDRA patterns found in the highest abundance were sequenced (31 total). Sequences related to aerobic bacteria (e.g., Nitrospira, Methylomonas, and Gallionella) predominated among those retrieved from the uncontaminated area of the site, whereas sequences related to facultatively aerobic and anaerobic bacteria (e.g. Azoarcus, Syntrophus, and Desulfotomaculum) predominated among those retrieved from contaminated areas of the site. Using NDO-specific primers and low-stringency PCR conditions, variability in RFLP patterns was only detected in community-derived DNA (3 of 4 wells) and not in 5 newly isolated naphthalene-degrading pure cultures. The ARDRA patterns of the pure culture isolates were not found in the clone libraries. Polymorphisms in community 16S rDNA and NDO genes found in well-water microorganisms reflected distinctive geochemical conditions across the site. Sequences related to sulfate-reducing bacteria were found in groundwater that contained sulfide, while sequences related to Gallionella, Syntrophus, and nitrate-reducing aromatic hydrocarbon-degrading bacteria were found in groundwater that contained ferrous iron, methane, and naphthalene, respectively.
Information on the type and amount of hazardous and toxic waste is required to develop a meaningful strategy and estimate a realistic cost for clean up of the Sydney Tar Pond site which is located on Cape Breton, in the province of Nova Scotia, Canada. The site covers the area of the decommissioned Sysco (Sydney Steel Corporation) plant. The materials of concern include BTEX (benzene, toluene, ethylbenzene, and xylenes), PAH (polycyclic aromatic hydrocarbons), PCB (polychlorinated biphenyl), and particulates laden with toxic metals, such as arsenic, lead, and others. The originally nontoxic materials such as soil, blast furnace slag, and vegetation, as well as surface and ground waters, which were subsequently contaminated, must also be included if they fail tests prescribed by environmental regulations. An extensive sampling program must be undertaken to obtain data for an accurate estimate of the waste to be cleaned and disposed of. Apparently, 700,000 tons of toxic waste, which is believed to be present on the site, may represent only a fraction of the actual amount. The clean-up of the site is only part of the solution. Toxic waste has to be disposed of in accordance with environmental regulations.
We have investigated the extent and pattern of immunostaining for the TAR DNA-binding protein, TDP-43, in 37 patients with frontotemporal lobar degeneration with ubiquitin (UBQ) pathology (FTLD-U). We confirm that TDP-43 protein is a component of the UBQ immunoreactive (UBQ-ir) neuronal cytoplasmic inclusions (NCI), neuronal intranuclear inclusions (NII) and neurites of the cerebral cortex and hippocampus in FTLD-U. We further show that the same three histological patterns, previously identified by us according to the form, number and distribution of the UBQ-ir NCI, NII and neurites are equivalently present in TDP-43 immunohistochemistry. TDP-43 immunoreactive (TDP-43-ir) NCI with rounded, spicular or skein-type appearance were seen in motor neurones of the trigeminal or facial cranial nerve nuclei in one patient with frontotemporal dementia (FTD) and in the spinal cord in three patients with FTD + motor neurone disease (MND). In patients with MND alone, TDP-43-ir NCI are common in anterior horn cells of the spinal cord, and occasionally seen in neurones of the hypoglossus nucleus. We show that TDP-43-ir NCI are also present within neurones in the superior and inferior olives in FTLD-U, and in some patients with MND. Although TDP-43 is normally seen as a nuclear protein, nuclear TDP-ir was not observed in neurones of the cerebral cortex, brainstem and spinal cord in FTLD-U or MND when NCI were present. We conclude that the UBQ-ir lesions of FTLD and MND are defined by the presence of TDP-43, and that these disorders can be subsumed into a single disease entity under the umbrella of TDP-43 proteinopathy.
A test system for the detection of substances with cell-irritating or cell-damaging effects using isolated brown fat cells is presented and the effects of cigarette smoke condensates (CSC) from high and low tar yield cigarettes on this system examined. The condensates inhibited noradrenaline stimulated respiration in a dose-dependent manner. Ethanol solutions of the condensates had a stronger inhibitory effect than DMSO solutions. The CSC strongly inhibited the mitochondrial function but other cellular functions were also impaired.
Since 1972, regular six-monthly surveys of cigarettes on sale in the UK have determined the yields of tar, nicotine and carbon monoxide in mainstream smoke. During 1983-1990, a series of special studies investigated the yields of a range of additional analytes and their inter-relationships with the routinely monitored components. The results for total cyanide (as hydrogen cyanide), total aldehydes (including acetaldehyde), acrolein, formaldehyde and nitrogen monoxide are summarized, and the full data for six low-molecular weight phenols and three polycyclic aromatic hydrocarbons (PAHs) are reported. It is concluded that with the exception of nitrogen monoxide, which is strongly dependent upon the type of tobacco, and the delivery of some phenols and PAHs, which may be affected to a minor extent by the design of cigarette, the three routinely monitored smoke components provide an adequate guide to the yields of the other analytes examined, across the range of manufactured cigarettes available in the UK in the 1980s.
Nuclear accumulation of the tumorsuppressor protein p53 indicates the occurrence of chromatin injury (J. Cancer Res. Clin. Oncol. 1991, 117, 30; Oncogene 1993, 8, 307) and may be used as an analytical tool to detect genotoxic agents. This mechanism was used to evaluate the DNA-damaging potency (clastogenicity) of the tar- and aerosol-free, gaseous phase of cigarette smoke which is obtained by filtration through Cambridge glass fiber filters. This condensate-free gas phase was absorbed by phosphate-buffered saline and immediately thereafter poured onto monolayers of the murine cell line L929 for 10 min. Eighteen hours later the nuclear accumulation of p53, an indicator for DNA damage, was determined. The elicited level of p53 was similar to that obtained by direct incubation with the gas phase of filtered cigarette smoke for 2 min or with several micrograms of mitomycin C per ml. Previous exhaustive filtration obviously does not inhibit the clastogenic property of tobacco smoke to exert severe DNA damage.
Productive infection with HIV-1, the virus responsible for AIDS, requires the involvement of host cell factors for completion of the replicative cycle, but the identification of these factors and elucidation of their specific functions has been difficult. A human cDNA, TRBP, was recently cloned and characterized as a positive regulator of gene expression that binds to the TAR region of the HIV-1 genome. Here we demonstrate that this factor is encoded by a gene, TARBP2, that maps to human chromosome 12 and mouse chromosome 15, and we also identify and map one human pseudogene (TARBP2P) and two mouse TRBP-related sequences (Tarbp2-rs1, Tarbp2-rs2). The map location of the expressed gene identifies it as a candidate for the previously identified factor encoded on human chromosome 12 that has been shown to be important for expression of HIV-1 genes. Western blotting indicates that despite high sequence conservation in human and mouse, the TARBP2 protein differs in apparent size in primate and rodent cells.
Besides generating novel binding peptides or small molecules to their RNA target, successful design of chemically modified RNA constructs capable of tighter binding with their binding peptides is also of significant importance. Herein, the synthesis and binding studies of a series of both wt and mutant bovine immunodeficiency virus (BIV) TAR RNA constructs against its Tat peptide are reported. Understanding the requirements that enable RNA construct binding properties, especially at the hairpin loop or internal bulge, would afford potential therapeutic approaches to control the BIV life cycle.
We have synthesized a series of phenothiazine derivatives, which were used to test the structure-activity relationship of binding to HIV-1 TAR RNA. Variations from our initial compound, 2-acetylphenothiazine, focused on two moieties: ring substitutions and n-alkyl substitutions. Binding characteristics were ascertained via NMR, principally by saturation transfer difference spectra of the ligand and imino proton resonance shifts of the RNA. Both ring and alkyl substitutions manifested NMR changes upon binding. In general, the active site, while somewhat flexible, has regions that can be capitalized for increased binding through van der Waals interactions and others that can be optimized for solubility in subsequent stages of development. However, binding can be nontrivially enhanced several-fold through optimization of van der Waals and hydrophilic sites of the scaffold.
For monitoring groundwater at tar oil contaminated sites a simple method of analysis was developed for the simultaneous detection of several NSO heterocyclic compounds, homocyclic compounds, mobile two- and three-cyclic PAHs and selected metabolites. The groundwater samples are enriched using SPE with polymer material at pH 4. Chromatographic separation and detection is performed by LC with diode array UV or fluorescence detection. The recoveries of 25 selected compounds were mostly between 80-110% and the detection limits were 0.4-2.4 microg/L for UV detection and for the fluorescence detectable compounds 0.4-140 ng/L. The method was successfully applied to groundwater samples from a wood preserving facility. Especially benzo(b)thiophene showed an increasing dominance downgradient of the source. Detection of metabolites, such as 1-hydroxyiso-, 2-hydroxyquinoline and 2-hydroxy-4-methylquinoline, 2-naphthoic acid, and 1-indanone, indicating in situ biodegradation, was confirmed by LC-ESI-MS analysis.
Water repellency can induce preferential flow and thus affect water flow and contaminant transport at hazardous waste sites. Since the spatial patterns of water repellency are mostly unknown, it is problematic to use numerical transport models to predict leachate composition. In this study, the spatial variability of soil water repellency was studied at an industrial site contaminated with tar oil, chromium, copper and arsenic. The persistence of water repellency was assessed by the water drop penetration time (WDPT), and the degree of water repellency was quantified by the ethanol percentage (EP) test. Measurements were made at the soil surface along 3.5-12.1 m long transects at different times between March and October 2002. The spatial variability of WDPT, EP, water content, and organic matter content was quantified by variogram analyses. Both the persistence and the degree of water repellency varied seasonally, with the highest water repellency during the summer months. The correlation lengths of WDPT values ranged between 16 and 406 cm, whereas EP values showed no spatial correlation. For field-moist samples, a critical soil water threshold, below which water repellency prevails, was estimated to be 2.5-4%. For oven dry samples, the WDPT values were dependent on the water content prior to drying. The wide range of correlation lengths and the temporal dynamics of spatial repellency patterns suggest that simulations of solute leaching must consider the spatial and temporal variability of soil hydrophobic properties.
Combinatorial therapies for the treatment of HIV-1 infection have proven to be effective in reducing patient viral loads and slowing the progression to AIDS. We have developed a series of RNA-based inhibitors for use in a gene therapy-based treatment for HIV-1 infection. The transcriptional units have been inserted into the backbone of a replication-defective lentiviral vector capable of transducing a wide array of cell types, including CD34+ hematopoietic progenitor cells. The combinatorial therapeutic RNA vector harbors a U6 Pol III promoter-driven short hairpin RNA (shRNA) targeting the rev and tat mRNAs of HIV-1, a U6 transcribed nucleolar-localizing TAR RNA decoy, and a VA1-derived Pol III cassette that expresses an anti-CCR5 ribozyme. Each of these therapeutic RNAs targets a different gene product and blocks HIV infection by a distinct mechanism. Our results demonstrate that the combinatorial vector suppresses HIV replication long term in a more-than-additive fashion relative to the single shRNA or double shRNA/ribozyme or decoy combinations. Our data demonstrate the validity and efficacy of a combinatorial RNA-based gene therapy for the treatment of HIV-1 infection.
Using molecular modelling studies, an active anti-HIV ethidium-arginine conjugate targeted against the viral TAR RNA sequence has been linked to an artificial ribonuclease, with the aim to obtain an irreversible inhibitor. The ribonuclease moiety consists of an N-[N-(3-aminopropyl)-3-aminopropyl] glycine and has been constructed via two successive N-alkylations following the Fukuyama procedure.
Real-time detection of air toxics is becoming increasingly important in understanding the sources and constituents of air pollution. The detection of low levels of air contaminants requires reliable sampling and calibration techniques, as well as sophisticated analytical instrumentation. Recently, a new low pressure chemical ionization (LPCI) source was developed for ambient air monitoring of benzene, toluene, xylene (BTX) and gas-phase polycyclic aromatic hydrocarbons (PAH) in real-time. This ion source in conjunction with a triple quadrupole (Q1, Q2, Q3) mass spectrometer (trace atmospheric gas analyzer (TAGA IIe)) has been proven highly useful for measuring selected air pollutants. The ion chemistry under LPCI conditions involves charge transfer reactions yielding parent ions which are selected in the first quadrupole, Q1, dissociated in the second quadrupole, Q2, and the resultant daughter ions are then identified by the third quadrupole, Q3. Monitoring of specific parent/daughter (P/D) ion pairs is used to measure concentrations of BTX and selected PAH. The response of the TAGA IIe is characterized through multi-point calibration curves. Detection limits (DL) as low as 0.5 microg/m(3) for BTX and PAH were accomplished by optimizing various TAGA IIe operating parameters. This unique method was applied in November 1999 to monitor emissions released during the cleanup of a historical coal tar site in Kingston, Ontario. This information was used by local officials for enhancing abatement activities or in some cases temporarily halting the excavation when levels of air toxics were higher than allowable provincial guidelines.
Wound botulism is a rare and potentially fatal disease. The use of black tar heroin has spawned an increase in the incidence of the disease, with the majority of cases occurring in California. The use of botulism antitoxin and surgical debridement are recommended to decrease hospital stay. For this to be effective, the diagnosis of wound botulism first must be considered, followed by an aggressive search for any area of infection that may be debrided. This case report demonstrates several factors to consider in patients presenting with symptoms of botulism poisoning: occurrence away from the Mexico border, no obvious abscess, and the need for prolonged ventilatory support. This case report documents a prolonged hospital stay, possibly caused by delay in administration of antitoxin in a patient with cellulitis that was not considered appropriate for debridement.
A 70-year-old woman with congenital absence of both radii but preservation of the thumb developed a marked pancytopenia after two i.v. injections of 1 g of 5-fluorouracil (5-FU) 1 week apart. She developed bloody diarrhoea after nine fractions of 2 Gy to parallel opposed 16 x 15 cm abdominal fields. This unusual response prompted an investigation of the radiosensitivity of the patient's cells by the sensitive G2 assay of transformed lymphocytes. The radiosensitivity of the patient's lymphoblastoid line appeared to be intermediate between that of normal individuals and an ataxia telangiectasia line. The clinical response and in vitro radiosensitivity testing suggest that the thrombocytopenia with absent radii (TAR) syndrome appears to be one of the inherited impaired DNA repair syndromes and is a very newly described radiation sensitivity syndrome. The development of three separate primary cancers in this patient (small bowel, ovary and bladder) suggests there is an increased risk of neoplasia in this condition.
Replication of human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all HIV mRNAs. A number of cyclic peptides are known to possess antibiotic activity and increased biological stability. Here we report the design, synthesis, and biological activity of a cyclic peptide (2), which inhibits transcriptional activation by Tat protein in human cells with an IC50 of approximately 40 nM. Cyclic peptides that can target specific RNA structures provide a new class of small molecules that can be used to control cellular processes involving RNA-protein interactions in vivo.