Orphan Site Research Articles

Commonly Used Therapeutics Associated with Changes in Arousal Inhibit GABAAR Activation.

GABAA receptor-positive modulators are well-known to induce sedation, sleep, and general anesthesia. Conversely, GABAA receptor negative allosteric modulators (GABAARNAMs) can increase arousal and induce seizures. Motivated by our studies with patients with hypersomnia, and our discovery that two GABAARNAMs can restore the Excitation/Inhibition (E/I) balance in vitro and arousal in vivo, we chose to screen 11 compounds that have been reported to modulate arousal, to see if they shared a GABA-related mechanism. We determined modulation with both conventional and microfluidic patch clamp methods. We found that receptor activation was variably modulated by all 11 compounds: Rifampicin (RIF), Metronidazole (MET), Minocycline (MIN), Erythromycin (ERY), Ofloxacin (OFX), Chloroquine (CQ), Hydroxychloroquine sulfate (HCQ), Flumazenil (FLZ), Pentylenetetrazol (PTZ), (-)-Epigallocatechin Gallate (EGCG), and clarithromycin (CLR). The computational modeling of modulator-receptor interactions predicted drug action at canonical binding sites and novel orphan sites on the receptor. Our findings suggest that multiple avenues of investigation are now open to investigate large and brain-penetrant molecules for the treatment of patients with diminished CNS E/I balance.

Assessment of contamination by rocket fuel components of remedied sites of silo launchers

Introduction. The use of highly toxic and highly hazardous components of liquid rocket fuel in silo-based intercontinental ballistic missiles makes it necessary to assure the health and epidemiological well-being of the population and environmental safety when eliminating silo launchers. The study aims to assess the chemical safety of the sites of silo launchers after their elimination by detonation and remediation of disturbed lands. Materials and methods. Samples of soil, water, vegetation were taken at 20 remedied sites of the former silo launchers of "single start" located in the Chelyabinsk region and the Altai Territory. These samples were analyzed in an accredited laboratory for the content of unsymmetrical dimethyl-hydrazine and its degradation products using certified photometric methods. Results. At the time of the survey in 2019, in 19 of 20 sites of former silo launchers, facts of unauthorized intrusion to the remedied sites were established in order to recover a scrap of non-ferrous and ferrous metals, building materials up to the depth of the location of the destroyed shafts of mine structures. In soil samples from 3 sites of silo launchers located in the Chelyabinsk region, asymmetric dimethyl-hydrazine was found in concentrations exceeding the MPC by 1.02 - 1.6 times. In water samples from open and water-flooded shafts of silo launchers, degradation products of unsymmetrical dimethyl-hydrazine were absent. Contamination of herbaceous and coniferous vegetation with asymmetric dimethyl-hydrazine at the surveyed sites has not been established. Conclusion. Soil contamination with asymmetric dimethyl-hydrazine at three remedied sites of 20 surveyed ones may be the result of their unauthorized opening. After the intrusion, the orphan sites of the silo launchers become objects of increased chemical hazard and environmental risk. Such things require carrying out nature restoration work, strengthening supervision over their technical, health and ecological condition.

Associations Between the Density of Oil and Gas Infrastructure and the Incidence, Stage and Outcomes of Solid Tumours: A Population-Based Geographic Analysis.

BackgroundWe hypothesized that there are geographic areas of increased cancer incidence in Alberta, and that these are associated with high densities of oil and gas(O+G) infrastructure. Our objective was to describe the relationship between O+G infrastructure and incidence of solid tumours on a population level.MethodsWe analyzed all patients >=18 years old with urological, breast, upper GI, colorectal, head and neck, hepatobiliary, lung, melanoma, and prostate cancers identified from the Alberta Cancer Registry from 2004-2016. Locations of active and orphan O+G sites were obtained from the Alberta Energy Regulator and Orphan Well Association. Orphan sites have no entity responsible for their maintenance. ArcGIS (ESRI, Toronto, Ontario) was used to calculate the distribution of O+G sites in each census distribution area (DA). Patient residence at diagnosis was defined by postal code. Incidence of cancer per DA was calculated and standardized. Negative binomial regression was done on O+G site density as a categorical variable with cutoffs of 1 and 30 wells/100km2, compared to areas with 0 sites.Results125,316 patients were identified in the study timeframe;58,243 (46.5%) were female, mean age 65.6 years. Breast (22%) and prostate (19.8%) cancers were most common. Mortality was 36.5% after a median of 30 months follow up (IQR 8.4 – 68.4). For categorical density of active O+G sites, RR was 1.02 for 1-30 sites/100km2 (95% CI=0.95-1.11) and 1.15 for >30 sites/100km2 (p<0.0001, 95%CI=1.11-1.2). For orphan sites, 1-30 sites RR was 1.25 (p<0.0001, 95%CI=1.16-1.36) and 1.01 (p=0.97, 95%CI=0.7-1.45) for >30 sites. For all O+G sites, RR for 1-30 sites was 1.03 (p=0.4328, 95%CI=0.95-1.11) and 1.15 (p<0.0001, 95%CI=1.11-1.2) for >30 sites.ConclusionWe report a statistically significant correlation between O+G infrastructure density and solid tumour incidence in Alberta. To our knowledge this is the first population-level study to observe that active and orphan O+G sites are associated with increased risk of solid tumours. This finding may inform policy on remediation and cancer prevention.

Mapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants

ABSTRACT In all eukaryotic cells, the most abundant modification of ribosomal RNA (rRNA) is methylation at the ribose moiety (2ʹ-O-methylation). Ribose methylation at specific rRNA sites is guided by small nucleolar RNAs (snoRNAs) of C/D-box type (C/D snoRNA) and achieved by the methyltransferase Fibrillarin (FIB). Here we used the Illumina-based RiboMethSeq approach for mapping rRNA 2ʹ-O-methylation sites in A. thaliana Col-0 (WT) plants. This analysis detected novel C/D snoRNA-guided rRNA 2ʹ-O-methylation positions and also some orphan sites without a matching C/D snoRNA. Furthermore, immunoprecipitation of Arabidopsis FIB2 identified and demonstrated expression of C/D snoRNAs corresponding to majority of mapped rRNA sites. On the other hand, we show that disruption of Arabidopsis Nucleolin 1 gene (NUC1), encoding a major nucleolar protein, decreases 2ʹ-O-methylation at specific rRNA sites suggesting functional/structural interconnections of 2ʹ-O-methylation with nucleolus organization and plant development. Finally, based on our findings and existent database sets, we introduce a new nomenclature system for C/D snoRNA in Arabidopsis plants.

Design and optimization of sustainable passive treatment systems for phosphogypsum leachates in an orphan disposal site

The optimization of the dispersed alkaline substrate (DAS) technology was investigated to achieve the treatment of highly acidic and polluted effluents from a phosphogypsum pile in an orphan site of SW Spain. This phosphogypsum disposal area is located on the Tinto river marsh soils, where it acts as a source of pollution for the estuarine environment, releasing high concentrations of metal(loid)s and radionuclides, which degrade the surrounding waters. The methodology consists of flowing the leachates through columns loaded with a combination of a fine-grained alkaline reagent scattered in a non-reactive matrix to raise the water pH while decreasing the solubility of dissolved contaminants. Seven columns were built, one for each of the alkaline reagent used: limestone, barium carbonate, biomass ash, fly ash, MgO, Mg(OH)2, and Ca(OH)2. The Ca(OH)2-DAS and MgO-DAS treatment systems showed the highest effectiveness, reaching near-total removal for PO4, F, Fe, Zn, Cu, Al, Cr, and U with initial reagent mass:treated volume ratios of 36.3 g/L and 7.57 g/L, respectively. Total As removal was only achieved in the Ca(OH)2-DAS treatment. Phosphate precipitation was the main mechanism responsible for pollutants removal. Geochemical modeling using PHREEQC code and mineralogical evidence confirmed the precipitation of these minerals. This study forms the basis of an effective and environmentally sustainable treatment system for phosphogypsum leachates to reduce the impact of the fertilizer industry worldwide.

Frequent interferon regulatory factor 1 (IRF1) binding at remote elements without histone modification

Transcriptional activators bind DNA and recruit cofactors to modify chromatin. The extent to which these two events are separable is unclear. Here, using a custom ChIP tiling array to map chromatin modifications, we show that interferon-γ-induced DNA binding of signal transducer and activator of transcription 1 (STAT1), typically associated with the transcription factor interferon regulatory factor 1 (IRF1), causes histone acetylation (H3ac, H4ac). In contrast, among IRF1 sites lacking concomitant STAT1 recruitment, only 25% underwent inducible histone acetylation, 31% exhibited constitutive histone acetylation, and 44% had no histone acetylation. These latter "orphan sites" also lacked other activating modifications (e.g. H3K4me1, H3K4me2) and were typically remote from transcription start sites. In these cases the closest gene was typically an IFNγ-inducible locus that did not respond to IFNγ in this setting. Orphan sites were detected in different cell types, suggesting broad relevance. Despite an atypical downstream response (i.e. no histone modifications), IRF1 binding depended on SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4 or BRG1), as is typical of active IRF1 enhancers. Although SMARCA4 permitted IRF1 access to the orphan sites, there was no corecruitment of the histone acetyltransferases CREB-binding protein (CBP) and p300. Orphan sites were constitutively unacetylated, and several were marked with repressive chromatin modifications (e.g. H3K27me3). In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.

Development Prospects of the Mangrove Relic of Foulpointe—East Madagascar

Located about fifty kilometers North of Toamasina (East Madagascar), the Commune of Mahavelona Foulpointe has a mangrove relic of about 2 hectares. Despite the ecological and socio-economic roles played by this ecosystem, it remains so far an orphan site, both in terms of official management and development. The purpose of this article is to take stock of the situation with a view to proposing methods for the sustainable development of this small mangrove via valuation of its natural dynamics. Systematic floristic inventory work was carried out, following a linear ABC transect of 50 - 100 m, from the sea (zone C) to the rear mangrove (zone A). Five mangrove species exist at Foulpointe: Avicennia marina, Sonneratia alba, Bruguiera gymnorrhiza, Rhizophora mucronata, Lumnitzera racemosa. With anthropogenic harvesting and tourism activities in the area, this ecosystem suffers an annual spatial loss of about 0.14 ha between 2009 and 2016. With a natural regeneration rate of about 966% the small man-grove has a strong capacity for regeneration. Taking into account the pace of current clearing, it would disappear in 10 - 15 years. The valorization of regenerated young plants, followed by intensive preservation and restoration actions, constitutes a sustainable development path.

Evolving Treatment Paradigms in Non-clear Cell Kidney Cancer.

With no therapy specifically approved for non-clear cell cancers of the kidney, this disease remains an orphan site. Clear cell renal cancers (ccRCC) have seen a flurry of activity with multiple agents gaining Food and Drug Administration (FDA) approval in recent years. Simultaneously, non-clear cell RCC (ncRCC) have also seen a fair share of activity and exploration of new agents in development but no specific FDA approvals. Non-clear cell RCC is a mixed bag of multiple types of tumors originating in the kidney with distinct clinical molecular and genetic characteristics that vary significantly from clear cell carcinoma of the kidney. Conventionally, non-clear cell RCC have been treated with the same therapies as clear cell RCC. The clinical trials are typically conducted in ccRCC and the FDA approval covers non-clear cell cancer as well. Few randomized clinical trials have been conducted specifically for ncRCC. With the advent of molecular and tumor genomic testing, leading to discovery of targets and associated therapies for ncRCC, a specific review of the state of management of this disease is timely and clinically relevant.

Tryptophan and Cysteine Mutations in M1 Helices of α1β3γ2L γ-Aminobutyric Acid Type A Receptors Indicate Distinct Intersubunit Sites for Four Intravenous Anesthetics and One Orphan Site.

γ-Aminobutyric acid type A (GABAA) receptors mediate important effects of intravenous general anesthetics. Photolabel derivatives of etomidate, propofol, barbiturates, and a neurosteroid get incorporated in GABAA receptor transmembrane helices M1 and M3 adjacent to intersubunit pockets. However, photolabels have not been consistently targeted at heteromeric αβγ receptors and do not form adducts with all contact residues. Complementary approaches may further define anesthetic sites in typical GABAA receptors. Two mutation-based strategies, substituted tryptophan sensitivity and substituted cysteine modification-protection, combined with voltage-clamp electrophysiology in Xenopus oocytes, were used to evaluate interactions between four intravenous anesthetics and six amino acids in M1 helices of α1, β3, and γ2L GABAA receptor subunits: two photolabeled residues, α1M236 and β3M227, and their homologs. Tryptophan substitutions at α1M236 and positional homologs β3L231 and γ2L246 all caused spontaneous channel gating and reduced γ-aminobutyric acid EC50. Substituted cysteine modification experiments indicated etomidate protection at α1L232C and α1M236C, R-5-allyl-1-methyl-5-(m-trifluoromethyl-diazirinylphenyl) barbituric acid protection at β3M227C and β3L231C, and propofol protection at α1M236C and β3M227C. No alphaxalone protection was evident at the residues the authors explored, and none of the tested anesthetics protected γ2I242C or γ2L246C. All five intersubunit transmembrane pockets of GABAA receptors display similar allosteric linkage to ion channel gating. Substituted cysteine modification and protection results were fully concordant with anesthetic photolabeling at α1M236 and β3M227 and revealed overlapping noncongruent sites for etomidate and propofol in β-α interfaces and R-5-allyl-1-methyl-5-(m-trifluoromethyl-diazirinylphenyl) barbituric acid and propofol in α-β and γ-β interfaces. The authors' results identify the α-γ transmembrane interface as a potentially unique orphan modulator site.

Acid mine drainage in the Iberian Pyrite Belt: 2. Lessons learned from recent passive remediation experiences

The Iberian Pyrite Belt (IPB), SW Spain and Portugal, contains about 100 abandoned mine wastes and galleries that release acid mine drainages (AMD) to the Tinto and Odiel rivers. In situ passive remediation technologies are especially suitable to remediate the drainages of these orphan sites. However, traditional remediation systems, designed for coal mines, have been demonstrated inefficient to treat the IPB mine waters. Due to their high acidity and metal loads, large amount of solids precipitate and fast clogging of porosity or passivation (coating) of the reactive grains occurs. To overcome these problems, the dispersed alkaline substrate (DAS) a mixture of fine-grained limestone sand and a coarse inert matrix (e.g., wood shavings) was developed. The small grains provide a large reactive surface and dissolve almost completely before the growing layer of precipitates passivates the substrate. The high porosity retards clogging. However, calcite dissolution only raises pH to values around 6.5, at which the hydroxides of trivalent metals (Al and Fe) precipitate, but it is not high enough to remove divalent metals. Caustic magnesia (MgO) buffers the solution pH between 8.5 and 10. A DAS system replacing limestone with caustic magnesia has been tested to be very efficient to remove divalent metals (Zn, Cd, Mn, Cu, Co, Ni, and Pb) from the water previously treated with calcite.

Interpreting the Contaminated Land Regime: Should the ‘Polluter’ Pay?

The contaminated land regime is not as effective as it could be. It is suggested that part of the reason for this is that enforcing authorities cannot afford to clean up land at a faster rate. Yet they are reluctant to recover their costs from Class B persons. There is evidence that local authorities believe that ‘innocent’ homeowners ought not to face the cost of remediation. This is, at least in part, because of a focus on the ‘polluter pays' principle. There seems to be a belief that, as they are not polluters, homeowners should not have to pay. Unfortunately this conclusion does not follow, leading to a misinterpretation of the ‘hardship test’ in section 78P of the Environmental Protection Act 1990. Instead, there should be a more explicit recognition that there are other principles in the background framework to the regime. In particular, the principle of stewardship provides a justification for homeowners to pay to remediate their land. If this is recognised, it is hoped that both local authorities and the Environment Agency will be encouraged to recover at least some of their costs from Class B persons which should free up funds to survey more land to determine levels of contamination, and to allow a clean-up of truly orphan sites.

Public policies for contaminated site cleanup: evidence from a survey of the Italian public

Cleaning up contaminated sites is currently considered one of the most important environmental policy priorities in many countries. Remediation of contaminated sites is attractive because it reduces risks to human health and ecological systems, and brings a host of potential social and economic benefits. Public programmes are deemed necessary by the law and in practice to address contamination at orphan site and to speed up the general processes of cleanups in most countries. People's opinion regarding these programmes in general and the priorities to be addressed is useful and pertinent given the large amount of resources to be devoted to the goal of remediation. In this work, we present the result of a national survey of the Italian public.

Contamined lands: a Canadian perspective

The existence of contaminated sites in Canada has become a problem of nation-wide concern. Actions at civil and common law based on the traditional requirements of showing that property interests have been affected or personal injury has resulted are inadequate to address widespread harms arising from pollution. At the national level programs and policies have been developed to address clean-up of contaminated sites. At the provincial level legislation is being developed, directed at making persons responsible for the pollution they cause. Nonetheless, there are shortcomings under the present system in matters concerning victim redress and clean-up and restoration of contaminated sites. Victims are still struggling to obtain redress and compensation, especially in cases of defendant bankruptcy. It may be necessary as in the U.S. to create a Superfund to ensure compensation when there are orphan sites or when the defendant has become insolvent. There may be merit in establishing at the Federal level and in the other provinces a class action scheme along the lines of the Quebec model with an Assistance Fund to help litigants. In addition, there is a need to develop in legislation comprehensive requirements of clean-up and restoration of contaminated sites, that can be applied consistently nation-wide.