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1.
Nature ; 534(7609): 705-9, 2016 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-27338791

RESUMO

Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinct cases in mammals (Tasmanian devils and dogs), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria) suggested that this phenomenon might be more widespread. Here we analyse disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and find that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species; however, unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographical area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers are found spreading within the species of origin, cross-species transmission of cancer cells can occur.


Assuntos
Doenças dos Animais/patologia , Doenças dos Animais/transmissão , Bivalves , Neoplasias/veterinária , Doenças dos Animais/diagnóstico , Doenças dos Animais/genética , Animais , Organismos Aquáticos/citologia , Bivalves/citologia , Bivalves/genética , Linhagem da Célula/genética , Núcleo Celular/genética , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Genótipo , Hemócitos/metabolismo , Neoplasias/diagnóstico , Neoplasias/genética , Neoplasias/patologia , Filogenia , Especificidade da Espécie
2.
Appl Microbiol Biotechnol ; 105(3): 1287-1300, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33443632

RESUMO

Biological treatment to remove dissolved selenium from mine-impacted water is often inhibited by the co-contaminant nitrate. In this work, we enriched microbial consortia capable of removing dissolved selenium in the presence of nitrate from native bacteria at sites influenced by coalmine seepages with elevated concentrations of Se, nitrate, and sulfate. Enrichments were collected from sediments in different vegetated or non-vegetated seepage collection ponds, and all demonstrated the potential for dissolved selenium removal. Nitrate inhibited dissolved selenium removal rates in four of these enrichments. However, microorganisms enriched from a mine seepage influenced natural vegetated marsh removed dissolved Se and nitrate simultaneously. Additionally, enrichments from one seepage collection pond achieved enhanced dissolved selenium removal in the presence of nitrate. Based on functional metagenomics, the dominant species with the metabolic capacity for selenate reduction were classified in Orders Enterobacterales and Clostridiales. Most putative selenate reductases identified as either ygfK, associated with selenoprotein synthesis or production of methylated organoselenium compounds, and narG, nitrate reductases with an affinity also for selenate.Key points• Enriched mine influenced sediment bacteria have the capacity for removal of dissolved Se species.• Consortia from a vegetated natural marsh reduced Se without inhibition from nitrate.• Nitrate stimulated the removal of Se by consortia from a disused tailing pond.


Assuntos
Compostos de Selênio , Selênio , Consórcios Microbianos , Nitratos , Ácido Selênico , Áreas Alagadas
3.
J Environ Manage ; 277: 111472, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-33049612

RESUMO

This study's aim was to compare biochar and steam activated biochar functionalized with iron for removal of selenium as selenate from solutions also containing nitrate and sulfate. The Fe-biochar composites were made impregnating iron (ferric nitrate) onto regular biochar (RB) and steam activated biochar (SAB), forming the Fe-biochar composites FeRB and FeSAB. Iron oxyhydroxide deposits were observed on the surface of FeRB using Raman spectroscopy analysis, but not on the FeSAB surface. Unmodified biochar samples did not remove selenium, as Se(VI), from solution, whereas FeRB and FeSAB recovered 8.3 mg-Se⋅g-composite-1 and 5.9 mg-Se⋅g-composite-1, respectively. Higher Se uptake was achieved at higher Fe-loads and lower acetone:biochar ratio, to a maximum of 17.3 mg-Se⋅g-composite-1 (FeRB). Washing after Fe-impregnation using deionized water diminished nitrate and Fe-leaching from the Fe-biochar composites while removing selenium. Se(VI) and sulfate uptake were observed when washed composites were tested in the presence of possible competing ions at environmentally relevant concentrations ([Se]t=0 = 1.01 ± 0.03 mg⋅L-1; [N-NO3-]t=0 = 40.2 ± 0.2 mg⋅L-1; and [SO42-]t=0 = 496 ± 25 mg⋅L-1). One of the possible mechanisms of removal might be the complexation of Se with the iron oxyhydroxide deposits (goethite and hematite) found on the FeRB surface.


Assuntos
Selênio , Poluentes Químicos da Água , Adsorção , Ânions , Carvão Vegetal , Poluentes Químicos da Água/análise
4.
J Environ Manage ; 222: 348-358, 2018 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-29870963

RESUMO

The mining industry needs to treat large volumes of wastewater highly concentrated in chemical compounds that can adversely affect receiving environments. One promising method of treatment is the use of reverse osmosis to remove most of the dissolved salts. However, the resulting brine reject is a highly saline wastewater that needs further treatment to remove the toxic components, such as selenate, which is a chemical compound of great concern in coal-mining regions. Biological reduction and removal of dissolved selenium from a brine solution was achieved. Microorganisms were enriched from environmental samples collected from two mines, respectively, at different geographic locations through adaptive evolution in the laboratory. Batch treatment of typical brine was tested with two different enrichments with the addition of either of two chemical forms of iron, ferrous chloride or zero valent iron. Successful selenium removal in the presence of high nitrate and sulphate concentrations was achieved with a combination of enriched microorganisms from one particular site and the addition of zero-valent iron. The composition and metabolic potential of the enriched microorganisms revealed Clostridium, Sphaerochaeta, Synergistes and Desulfosporosinus species with the metabolic potential for selenate reduction through the YgfK enzymatic process associated with selenium detoxification.


Assuntos
Bactérias Anaeróbias , Ácido Selênico/isolamento & purificação , Poluentes Químicos da Água/isolamento & purificação , Ferro , Sais , Ácido Selênico/metabolismo , Poluentes Químicos da Água/metabolismo
5.
Water Sci Technol ; 72(6): 875-81, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26360746

RESUMO

Successful operation of sulphate-reducing bioreactors using complex organic materials depends on providing a balance between more easily degrading material that achieves reasonable kinetics and low hydraulic retention times, and more slowly decomposing material that sustains performance in the long term. In this study, two organic mixtures containing the same ingredients typical of bioreactors used at mine sites (woodchips, hay and cow manure) but with different ratios of wood (recalcitrant) to hay (labile) were tested in six continuous flow bioreactors treating synthetic mine-affected water containing 600 mg/L of sulphate and 15 µg/L of selenium. The reactors were operated for short (5-6 months) and long (435-450 days) periods of time at the same hydraulic retention time of 15 days. There were no differences in the performance of the bioreactors in terms of sulphate-reduction over the short term, but the wood-rich bioreactors experienced variable and sometimes unreliable sulphate-reduction over the long term. Presence of more hay in the organic mixture was able to better sustain reliable performance. Production of dissolved organic compounds due to biodegradation within the bioreactors was detected for the first 175-230 days, after which their depletion coincided with a crash phase observed in the wood-rich bioreactors only.


Assuntos
Reatores Biológicos , Selênio/metabolismo , Sulfatos/metabolismo , Animais , Biodegradação Ambiental , Bovinos , Feminino , Esterco/análise , Compostos Orgânicos/análise , Selênio/química , Compostos de Selênio , Sulfatos/química , Madeira/química
6.
J Invertebr Pathol ; 117: 68-72, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24576571

RESUMO

Flow cytometry was investigated as an alternative to visual haemocytology for potentially higher-throughput and less subjective detection of neoplasia in Mytilus trossulus. In contrast to previous studies of ploidy in the Mytilus spp. complex, distinct tetra- and pentaploidal neoplastic cells were rare and a wide range of aneuploidy peaks from 1.4n to 5.5n were detected for late-stage leukemic animals. There was no correlation between aneuploidy and the number of diseased cells for early and intermediate disease stages. Formation of aneuploidy and neoplasia progression might not be simultaneous, and DNA content analysis using flow cytometry was only useful for detecting late stages of the disease.


Assuntos
Citometria de Fluxo/métodos , Hemócitos/patologia , Mytilus , Animais , Colúmbia Britânica , Ploidias
7.
Heliyon ; 10(3): e24914, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38317929

RESUMO

Understanding the impact of various parameters on the kinetics of dissolved selenium (Se) removal in bioreactors can be a challenging task, primarily due to the mass transfer limitations inherent in bioreactors employing attached growth configurations. This study successfully established a proof-of-concept for the efficient removal of Se from aqueous solutions using a chemostat bioreactor that relies solely on suspended growth. The research investigated the effect of selenate-Se feed concentrations under two distinct Se concentration conditions. One experiment was conducted at a considerably elevated concentration of 25 mg/L to impose stress on the system and evaluate its response. Another experiment replicated an environmentally relevant concentration of 1 mg/L, mirroring the typical Se concentrations in mine water. The bioreactor, featuring a working volume of 0.35 L, was operated as an anaerobic, fully mixed chemostat with hydraulic retention times (HRTs) ranging from 5 to 0.25 days. The outcomes revealed the chemostat's capacity to remove up to 25 mg/L of dissolved Se from water for all HRTs exceeding 1 day, under otherwise optimal conditions encompassing temperature, pH, and salinity. The research's significance lies in the development of a versatile tool designed to examine Se removal kinetics within a system devoid of mass transfer limitations. Furthermore, this study verified the ability of the bacterial consortium, obtained from a mine-influenced environment and enriched in the laboratory, to grow and sustain Se removal activities within a chemostat operating with HRTs as short as 1 day.

8.
J Environ Manage ; 119: 29-35, 2013 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-23435183

RESUMO

End-product from 16 public mixed latrine style composting toilets (CTs) at 12 sites between 50 and 2100 m.a.s.l. in Western North America was tested in order to evaluate the effect of composting variables (TS%, NH3-N, temperature, and material age) on compost quality and hygiene (VS%, Escherichia coli, [Formula: see text] -N, and pH). Principal component analysis indicated that TS%, temperature, and material age equally contributed to reduction in VS%. NH3-N had the greatest effect on [Formula: see text] -N, E. coli, and pH. Nitrification was significantly inhibited above 386 mg/kg NH3-N, but no such limit was found for E. coli, despite a significant (p = 0.016) but weak (r(2) = 0.11) negative relationship. It may be possible to amplify the sanitizing effect of ammonia and overcome pathogen resistance due to low temperatures and re-contamination (caused by poor design) with generous dosing of urea and ash. However, even sanitized, the fertilization effect of discharged material on the natural environment may not be desired or permitted in parks or protected areas where many CTs were found. To this end, operators of CTs need to evaluate their primary management objectives and ensure congruency with proven system capabilities.


Assuntos
Eliminação de Resíduos/métodos , Resíduos Sólidos/análise , Banheiros , Amônia/análise , Amônia/metabolismo , Canadá , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Escherichia coli/metabolismo , Concentração de Íons de Hidrogênio , Análise Multivariada , Nitratos/análise , Nitratos/metabolismo , Temperatura , Fatores de Tempo , Washington
9.
iScience ; 26(11): 108006, 2023 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-37876820

RESUMO

Protein biomarkers can be used to characterize symptom classes, which describe the metabolic or immunodeficient state of patients during the progression of a specific disease. Recent literature has shown that machine learning methods can complement traditional clinical methods in identifying biomarkers. However, many machine learning frameworks only apply narrowly to a specific archetype or subset of diseases. In this paper, we propose a feature extractor which can discover protein biomarkers for a wide variety of classification problems. The feature extractor uses a special type of deep learning model, which discovers a latent space that allows for optimal class separation and enhanced class cluster identity. The extracted biomarkers can then be used to train highly accurate supervised learning models. We apply our methods to a dataset involving COVID-19 patients and another involving scleroderma patients, to demonstrate improved class separation and reduced false discovery rates compared to results obtained using traditional models.

10.
PLoS One ; 16(9): e0256782, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34506523

RESUMO

Much of the current research on supervised modelling is focused on maximizing outcome prediction accuracy. However, in engineering disciplines, an arguably more important goal is that of feature extraction, the identification of relevant features associated with the various outcomes. For instance, in microbial communities, the identification of keystone species can often lead to improved prediction of future behavioral shifts. This paper proposes a novel feature extractor based on Deep Learning, which is largely agnostic to underlying assumptions regarding the training data. Starting from a collection of microbial species abundance counts, the Deep Learning model first trains itself to classify the selected distinct habitats. It then identifies indicator species associated with the habitats. The results are then compared and contrasted with those obtained by traditional statistical techniques. The indicator species are similar when compared at top taxonomic levels such as Domain and Phylum, despite visible differences in lower levels such as Class and Order. More importantly, when our estimated indicators are used to predict final habitat labels using simpler models (such as Support Vector Machines and traditional Artificial Neural Networks), the prediction accuracy is improved. Overall, this study serves as a preliminary step that bridges modern, black-box Machine Learning models with traditional, domain expertise-rich techniques.


Assuntos
Aprendizado Profundo , Ecossistema , Máquina de Vetores de Suporte
11.
Mutat Res ; 701(2): 145-52, 2010 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-20541620

RESUMO

Several bivalve species, including mussels (Mytilus spp.) and clams (Mya spp.), are susceptible to a leukemia-like disease called haemic neoplasia that has been known to decimate whole populations. Previous studies of molecular processes associated with late stages of this disease have implicated analogs of the p53 tumour suppressor protein family in disease etiology. We detected synonymous single nucleotide polymorphisms (SNPs) in the coding region sequence of p53-like cDNA from Mytilus trossulus (bay mussel) that differ between normal and neoplastic haemolymph. SNPs were located at positions 182, 392 and 821 bp. Most (94%) of the late leukemic animals sampled from cages in Burrard Inlet (British Columbia, Canada) had the same p53-like genotype, C182T G392G C821T, whereas 75% of the healthy animals were homozygous at positions C182C and T821T, independent of the genotype at the 392 bp position. As well, we detected an increased number of allelic variants in the leukemic animals that may arise from separate somatic mutation events in haemocyte precursors or from additional p53-like gene copies in polyploidy. Therefore, detection of these SNPs may provide a useful genetic biomarker for efficient monitoring of mussel population health.


Assuntos
Bivalves/genética , DNA Complementar , Genes p53 , Animais , Sequência de Bases , Bivalves/citologia , Hemócitos/ultraestrutura , Leucemia/genética , Polimorfismo de Nucleotídeo Único
12.
Environ Microbiol ; 11(12): 3233-51, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19735278

RESUMO

At two stations surveyed in Nitinat Lake, a approximately 200-m-deep anoxic tidal fjord, sulfide was detected as close as 15 m from the surface. Biological characterization, determined from small subunit ribosomal RNA gene sequencing, of the chemocline and anaerobic zone revealed many sequences related to sulfur-oxidizing bacteria, suggesting that sulfur cycling is a dominant process. gamma- and epsilon-Proteobacteria related to thiotrophic symbionts, as well as Chlorobium sp., dominated the transition zone. These are expected to play a role in dark and phototrophic CO(2) fixation, respectively. epsilon-Proteobacteria phylotype abundance increased with depth, eventually comprising 69-97% of all sequences recovered from the anoxic zone. The vast majority (74%) of these phylotypes were affiliated with a novel Acrobacter sp. group (NITEP5). Quantification of NITEP5 revealed that up to 2.8 x 10(5) cells ml(-1) were present in the anoxic zone. Surprisingly, although sequences related to known sulfate-reducing bacteria were recovered from the transition zone, quantification of the dsr gene and (35)SO(4)(2-) uptake tests suggest that sulfate-reduction within the water column is negligible. Overall, sequence diversity between different vertical zones was high, although the spatial segregation of gamma-Proteobacteria, Chlorobi, and epsilon-Proteobacteria did not appear to vary significantly between seasons.


Assuntos
Bactérias/classificação , Biodiversidade , Água Doce/microbiologia , Filogenia , Bactérias/genética , Bactérias/isolamento & purificação , Canadá , Chlorobium/classificação , Chlorobium/genética , Chlorobium/isolamento & purificação , Epsilonproteobacteria/classificação , Epsilonproteobacteria/isolamento & purificação , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Genes Bacterianos , Variação Genética , Geografia
13.
Elife ; 82019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31686650

RESUMO

Transmissible cancers, in which cancer cells themselves act as an infectious agent, have been identified in Tasmanian devils, dogs, and four bivalves. We investigated a disseminated neoplasia affecting geographically distant populations of two species of mussels (Mytilus chilensis in South America and M. edulis in Europe). Sequencing alleles from four loci (two nuclear and two mitochondrial) provided evidence of transmissible cancer in both species. Phylogenetic analysis of cancer-associated alleles and analysis of diagnostic SNPs showed that cancers in both species likely arose in a third species of mussel (M. trossulus), but these cancer cells are independent from the previously identified transmissible cancer in M. trossulus from Canada. Unexpectedly, cancers from M. chilensis and M. edulis are nearly identical, showing that the same cancer lineage affects both. Thus, a single transmissible cancer lineage has crossed into two new host species and has been transferred across the Atlantic and Pacific Oceans and between the Northern and Southern hemispheres.


Assuntos
Organismos Aquáticos , Mytilus , Neoplasias/veterinária , Alelos , Animais , Europa (Continente)/epidemiologia , Neoplasias/epidemiologia , Neoplasias/patologia , Filogenia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , América do Sul/epidemiologia
14.
Mar Environ Res ; 66(4): 412-21, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18653229

RESUMO

Mussels of the genus Mytilus are widely used in environmental monitoring. They can develop a leukaemia-like disease, haemic neoplasia, which could be induced, in part, by environmental stressors. The molluscan p53 tumor suppressor gene family was previously shown to be involved in haemic neoplasia at the protein level. The purpose of this study was the quantification of molluscan p53-like isoforms at the mRNA level in mussels with haemic neoplasia compared to normal controls. The three isoforms monitored were a p53-like, a TAp63/73-like containing an intact transactivation (TA) domain, and an NH(2)-terminally truncated p63/73 isoform termed DeltaNp63/p73-like that lacks the full TA domain. Using a comprehensive data set of 62 individual Mytilus trossulus and reverse transcription real-time PCR, we found that both the p53 and the DeltaNp63/73 isoforms were up-regulated in neoplastic haemocytes compared to normal haemocytes (p<0.0001). In contrast, the mRNA levels of the non-truncated isoform TAp63/73 did not change significantly in mussels with the disease at alpha=0.01 (p=0.0141), in contrast to previous findings at the protein level. Correlations in mRNA levels between the truncated isoform and the full-length isoforms in normal haemocytes were lost in neoplastic haemocytes. The increase in mRNA concentration of the truncated DeltaNp63/73 isoform in molluscan haemic neoplasia is similar to observations in many human cancers and cell lines and underlines the phylogenetically ancient oncogenic role of this isoform.


Assuntos
Regulação Neoplásica da Expressão Gênica , Genes p53/genética , Hemócitos/patologia , Mytilus/metabolismo , RNA Mensageiro/genética , Animais , Hemócitos/metabolismo , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa
15.
Microorganisms ; 6(1)2018 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-29473875

RESUMO

Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.

16.
Water Res ; 140: 268-279, 2018 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-29723816

RESUMO

Mine drainage contaminated with metals is a major environmental threat since it is a source of water pollution with devastating effects on aquatic ecosystems. Conventional active treatment technologies are prohibitively expensive and so there is increasing demand to develop reliable, cost-effective and sustainable passive or semi-passive treatment. These are promising alternatives since they leverage the metabolism of microorganisms native to the disturbed site at in situ or close to in situ conditions. Since this is a biological approach, it is not clear if semi-passive treatment would be effective in remote locations with extremely cold weather such as at mines in the subarctic. In this study we tested the hypothesis that sulfate-reducing bacteria, which are microorganisms that promote metal precipitation, exist in subarctic mine environments and their activity can be stimulated by adding a readily available carbon source. An experiment was setup at a closed mine in the Yukon Territory, Canada, where leaching of Zn and Cd occurs. To test if semi-passive treatment could precipitate these metals and prevent further leaching from waste rock, molasses as a carbon source was added to anaerobic bioreactors mimicking the belowground in-situ conditions. Microbial community analysis confirmed that sulfate-reducing bacteria became enriched in the bioreactors upon addition of molasses. The population composition remained fairly stable over the 14 month operating period despite temperature shifts from 17 to 5 °C. Sulfate reduction functionality was confirmed by quantification of the gene for dissimilatory sulfite reductase. Metals were removed from underground mine drainage fed into the bioreactors with Zn removal efficiency varying between 20.9% in winter and 89.3% in summer, and Cd removal efficiency between 39% in winter and 90.5% in summer. This study demonstrated that stimulation of native SRB in MIW was possible and that in situ semi-passive treatment can be effective in removing metals despite the cold climate.


Assuntos
Reatores Biológicos , Metais/metabolismo , Sulfatos/metabolismo , Poluentes Químicos da Água/química , Purificação da Água/métodos , Reatores Biológicos/microbiologia , Metais/química , Consórcios Microbianos/genética , Consórcios Microbianos/fisiologia , Mineração , Melaço , Oxirredutases atuantes sobre Doadores de Grupo Enxofre/genética , Filogenia , RNA Ribossômico 16S , Sulfatos/química , Óxidos de Enxofre , Poluentes Químicos da Água/metabolismo , Purificação da Água/instrumentação , Yukon
17.
PLoS One ; 13(4): e0196032, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29694379

RESUMO

We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.


Assuntos
Bactérias/classificação , Metagenômica/métodos , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Concentração de Íons de Hidrogênio , Mineração , Nitratos/metabolismo , Análise de Sequência de DNA , Solo/química , Água/química , Áreas Alagadas
18.
Mar Biotechnol (NY) ; 9(2): 217-30, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17242983

RESUMO

The p53 family of transcription factors has been implicated in many vertebrate cancers. Altered p53 and p73 protein expression observed in leukemic cells of molluscs suggests that these transcription factors might be involved in invertebrate cancers as well. Here, we fully characterize the mRNA of four novel p53-like variants in the bivalve molluscs Mytilus trossulus (bay mussel) and Mytilus edulis (blue mussel). These species, widely used for environmental assessment, develop a hemic neoplasia (leukemia) that is frequently fatal. The correlation between expression of p53 and its close relative p73 and onset of molluscan leukemia was documented previously. We report the sequences of two distinct and novel p63/p73-like mRNAs, amplified by polymerase chain reaction (PCR) from both species. One of the p63/p73-like isoforms contains a 360 nt truncation in the 5' coding region. Based on this truncation and concomitant lack of a transactivation (TA) domain, we designate this variant as a DeltaNp63/p73-like isoform: the first to be reported in an invertebrate species. In mammalian species, DeltaNp73 potently inhibits the tumor-suppressive function of p73 and p53, and its overexpression serves as a robust marker for mammalian cancer. In addition, we report on the occurrence of alternate polyadenylation sites in the molluscan p63/p73: one proximal and one distal site, which differ by 1260 nt. We hypothesize that differential expression of various molluscan p63/p73-like isoforms, controlled in part by polyadenylation site choice variation, may help to interpret the apparently opposing roles of this gene in the development of cancer. Overall, this research further illustrates the utility of the molluscan model for studies involving the molecular mechanisms of oncogenesis in naturally occurring populations. The data presented here require a revisiting of hypotheses regarding evolution of the p53 gene family. Current hypotheses indicate that (1) the protostome gene family does not contain an intronic promoter for DeltaN expression and (2) p53 gene duplication did not occur in protostomes. Our characterization of DeltaN p63/73 in mussel suggests that molluscan p53 gene family members have acquired an intronic promoter or splicing mechanism, either by invention that predates the evolutionary split of deuterostomes from protostomes, or by parallel evolution. Our data also show that Mytilus p53, p63/p73, and DeltaNp63/p73 are identical in their core regions with variation limited to their C- and N-terminals, supporting the notion that alternative splicing, intronic promoter usage, and polyadenylation site choice may lead to expression of distinct isoforms originating from one common gene.


Assuntos
Mytilus/fisiologia , Proteínas Supressoras de Tumor/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Primers do DNA/química , DNA Espaçador Ribossômico/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Dados de Sequência Molecular , Mytilus edulis/fisiologia , Proteínas Nucleares/química , Proteínas Nucleares/genética , Filogenia , Poliadenilação/genética , Polimorfismo de Fragmento de Restrição , Isoformas de Proteínas/genética , RNA Mensageiro/química , Alinhamento de Sequência , Análise de Sequência de Proteína/veterinária , Proteína Tumoral p73 , Proteína Supressora de Tumor p53/química , Proteína Supressora de Tumor p53/genética , Proteínas Supressoras de Tumor/química
19.
Chemosphere ; 183: 536-545, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28570897

RESUMO

Increasing selenium concentrations in aquatic environments downstream of mine sites is of great concern due to selenium's bioaccumulation propensity and teratogenic toxicity. Removal of selenium from mine influenced water is complicated by the presence of nitrate, which is also elevated in mine influenced water due to the use of explosives in mining. In many biological treatment processes, nitrate as a thermodynamically more preferable electron acceptor inhibits selenate reduction. Here we report on an enrichment of a bacterial assemblage from a mine impacted natural marsh sediment that was capable of simultaneous selenate reduction and denitrification. Selenate reduction followed first order kinetics with respect to the concentration of total dissolved selenium. The kinetic rate constant was independent of initial nitrate concentration over the range 3-143 mg L-1-NO3--N. The initial concentration of selenate inhibited selenate reduction kinetics over the range 1-24 mg-Se L-1. Dominant taxa that grew in selenate only medium were classified in the genera Pseudomonas, Lysinibacillus and Thauera. When nitrate was introduced in addition to selenate, previously rare taxa that became dominant were relatives of Exiguobacterium, Tissierella and Clostridium. Open reading frames (ORFs) associated with dissimilatory denitrification were identified for Pseudomonas, Thauera and Clostridium. In addition, ORFs were found that were homologous with known selenate reductase subunits (SerA and SerB). These findings suggest that native mine site bacteria can be used for removing selenate and nitrate from mine wastewater.


Assuntos
Consórcios Microbianos , Mineração , Nitratos/análise , Ácido Selênico/análise , Poluentes Químicos da Água/análise , Purificação da Água/métodos , Bactérias Anaeróbias/genética , Bactérias Anaeróbias/crescimento & desenvolvimento , Desnitrificação , Cinética , Oxirredução , Oxirredutases/genética
20.
Waste Manag ; 33(7): 1602-6, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23647950

RESUMO

It is challenging and expensive to monitor and test decentralized composting toilet systems, yet critical to prevent the mismanagement of potentially harmful and pathogenic end-product. Recent studies indicate that mixed latrine composting toilets can be inhibited by high ammonia content, a product of urea hydrolysis. Urine-diverting vermicomposting toilets are better able to accomplish the goals of remote site human waste management by facilitating the consumption of fecal matter by earthworms, which are highly sensitive to ammonia. The reliability of Solvita compost stability and maturity tests were evaluated as a means of determining feedstock suitability for vermicomposting (ammonia) and end-product stability/completeness (carbon dioxide). A significant linear regression between Solvita ammonia and free ammonia gas was found. Solvita ranking of maturity did not correspond to ranking assigned by ammonium:nitrate standards. Solvita ammonia values 4 and 5 contained ammonia levels below earthworm toxicity limits in 80% and 100% of samples respectively indicative of their use in evaluating feedstock suitability for vermicomposting. Solvita stability tests did not correlate with carbon dioxide evolution tests nor ranking of stability by the same test, presumably due to in situ inhibition of decomposition and microbial respiration by ammonia which were reported by the Solvita CO2 test as having high stability values.


Assuntos
Eliminação de Resíduos/métodos , Solo , Banheiros , Amônia , Animais , Dióxido de Carbono , Fezes , Humanos , Nitratos , Oligoquetos
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