Relevant bibliographies by topics / Microbial samples

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Academic literature on the topic 'Microbial samples'

Author: Grafiati
Published: 28 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Microbial samples"

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Fierer, Noah, and Craig Cary. "Don't let microbial samples perish." Nature 512, no. 7514 (August 2014): 253. http://dx.doi.org/10.1038/512253b.

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Haas, Charles N. "Microbial Sampling: Is It Better to Sample Many Times or Use Large Samples?" Water Science and Technology 27, no. 3-4 (February 1, 1993): 19–25. http://dx.doi.org/10.2166/wst.1993.0314.

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Repeated sampling of a water (raw, Ssished, recreational) is often used to assess microbial quality. Microbial distributions have often been found to be negative binomial distributed in such repeated samples. Under these conditions, it is shown that it is better to use a large number of small volume samples than vice versa, providing that the negative binomial dispersion parameter remains unaffected by volume. Further research is needed to determine if the latter assumption, which influences the conclusion proposed, is valid for various classes of microorganisms in various types of waters.
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Sharifullina, D. M., R. M. Vasil’eva, T. I. Yakovleva, E. G. Nikolaeva, O. K. Pozdeev, A. P. Lozhkin, and R. N. Khayrullin. "Microbial landscape of atherosclerotic plaques biopsy samples." Kazan medical journal 96, no. 6 (December 15, 2015): 979–82. http://dx.doi.org/10.17750/kmj2015-979.

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Aim. To study the microflora composition of different localization atherosclerotic plaques in patients with atherosclerosis. Methods. 88 samples of atherosclerotic plaques were analyzed, including brachycephalic arteries - 71, the coronary arteries - 13, the aorta - 2, vessels of lower extremities - 2. The specimens were obtained from 71 men and 17 women aged 30-79 years (mean age 50.8 years). The presence of aerobic and anaerobic microflora was determined by bacteriological method. Detection of the cytomegalovirus nucleic acid, herpes simplex virus types 1 and 2, Epstein-Barr virus was performed by real time polymerase chain reaction. Results. The most diverse microflora was represented in the plaques of the neck vessels (carotid arteries). Thereat we found bacteria in 77.5% of the samples, including Propionibacterium acnes - 40.8%, the Staphylococcus genus - 50.7%. 83.3% Staphylococcus isolates were identified as S. epidermidis. In 14.1% of the samples from the brachycephalic artery plaques microorganisms associations (P. acnes and S. epidermidis) were found. The coronary arteries and aorta plaques microflora was represented entirely by P. acnes - 15.4 and 50% respectively. Herpes simplex virus type 1 and 2, and Epstein-Barr virus nucleic acids were detected in 6.7% of samples of carotid artery atherosclerotic plaques. Bacteria associations were presented exclusively in atherosclerotic plaques from brachycephalic arteries - 11.4% of the samples, including 9 bacteria (P. acnes and S. epidermidis) associations, and one association consisted of 3 microorganisms: 2 bacteria (P. acnes and S. epidermidis) and the virus (Epstein-Barr virus). Conclusion. Observed high frequency of microorganisms detection in studied atherosclerotic plaques samples allows to suggest their possible pathogenetic role in the blood vessels endothelium atherosclerotic lesions formation.
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Ciafardini, G., and B. A. Zullo. "Assay of microbial enzymes in opaque samples." Journal of Microbiological Methods 34, no. 1 (September 1998): 73–79. http://dx.doi.org/10.1016/s0167-7012(98)00071-2.

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Hyvärinen, A., H. Rintala, S. Kokkonen, L. Larsson, and A. Nevalainen. "Microbial Exposure Assessment With House Dust Samples." Epidemiology 17, Suppl (November 2006): S227. http://dx.doi.org/10.1097/00001648-200611001-00582.

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Jufri, Rhezqy Furwati. "Microbial Isolation." Journal La Lifesci 1, no. 1 (January 30, 2020): 18–23. http://dx.doi.org/10.37899/journallalifesci.v1i1.33.

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The importance of isolating a microbe from the environment, such as food (solid substrate), drinks (liquid substrate), and yourself because of the many microbes that are difficult to observe or distinguish directly using the five senses. A sample can contain bacteria or fungi. By isolating, the shape of the colonies and the contents in a sample can be observed. Bacteria from the air and normal flora form colonies with lobate-shaped edges, whereas bacteria found in well water samples form colonies with irregular edges and there are also fungi found in the well water samples.
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Berthod, Alain, Mike A. Rodriguez, Marco Girod, and Daniel W. Armstrong. "Use of microbubbles in capillary electrophoresis for sample segregation when focusing microbial samples." Journal of Separation Science 25, no. 15-17 (November 1, 2002): 988–95. http://dx.doi.org/10.1002/1615-9314(20021101)25:15/17<988::aid-jssc988>3.0.co;2-i.

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Clarke, Erik L., Abigail P. Lauder, Casey E. Hofstaedter, Young Hwang, Ayannah S. Fitzgerald, Ize Imai, Wojciech Biernat, et al. "Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low–Microbial Content Samples." American Journal of Respiratory and Critical Care Medicine 197, no. 2 (January 15, 2018): 225–34. http://dx.doi.org/10.1164/rccm.201705-0891oc.

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Poretsky, Rachel S., Nasreen Bano, Alison Buchan, Gary LeCleir, Jutta Kleikemper, Maria Pickering, Whitney M. Pate, Mary Ann Moran, and James T. Hollibaugh. "Analysis of Microbial Gene Transcripts in Environmental Samples†." Applied and Environmental Microbiology 71, no. 7 (July 2005): 4121–26. http://dx.doi.org/10.1128/aem.71.7.4121-4126.2005.

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ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.
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Webster, JoAnn J., Ginger J. Hampton, John T. Wilson, William C. Ghiorse, and Franklin R. Leach. "Determination of Microbial Cell Numbers in Subsurface Samples." Ground Water 23, no. 1 (January 1985): 17–25. http://dx.doi.org/10.1111/j.1745-6584.1985.tb02775.x.

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Dissertations / Theses on the topic "Microbial samples"

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Allevi, Richard Paul. "Quantifying Potential Sources of Microbial Contamination in Household Drinking Water Samples." Thesis, Virginia Tech, 2012. http://hdl.handle.net/10919/42011.

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In Virginia, over one million households rely on private water supplies (e.g. well, spring, cistern). Previous literature acknowledges bacterial contamination in private water supplies as a significant public health concern in the United States. The present study tested private wells and springs in 20 Virginia counties for total coliforms (TC) and E. coli (EC) along with a suite of chemical contaminants. Sample collection was organized by the Virginia Household Water Quality Program (VAHWQP), a Virginia Cooperative Extension effort managed by faculty in the Biological Systems Engineering Department. Microbial and chemical source tracking were used to identify possible sources of contamination. A logistic regression was employed to investigate potential correlations between TC contamination and chemical parameters (e.g. NO3-, turbidity) as well as homeowner provided survey data describing system characteristics and perceived water quality. TC and EC contamination were quantified via the Colilert (www.idexx.com) defined substrate method for most probable number (MPN) of EC and TC per 100 mL of water. Of the 538 samples collected, 41% (n=221) were positive for TC and 10% (n=53) for EC. Chemical parameters were not statistically predictive of microbial contamination. Well depth, water treatment, and farm location proximate to the water supply were factors in a regression model that predicted presence/absence of TC with 74% accuracy. Microbial and chemical source tracking techniques (Polymerase Chain Reaction (PCR) and fluorometry, respectively) identified 4 of 26 samples as likely contaminated with human wastewater. Application of these source-tracking analyses on a larger scale will prove useful in defining remediation strategies.
Master of Science
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Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.

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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host. The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population. With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.
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Morin, Felix. "Development and Environmental Application of Microbial Bioreporters of Oxidative Stress." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/33027.

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There is a need for a sensitive, specific, rapid and cost-effective assay that can be used as an early warning signal of contamination of aquatic ecosystems. The purpose of this work was to develop a sensitive stress-specific microbial bioreporter responsive to pro-oxidants. Furthermore, the bioreporter was designed to be applicable in environments possibly affected by metal processing activities. An E.coli bioreporter was developed containing a plasmid with the katG promoter sequence as the sensing sequence and with mCherry as the reporter protein. The bioreporter responded to metal pro-oxidants (Cd, As, Zn, Pb, Ag and Ag nanoparticles). A new assay growth-medium was developed and contributed to improve the sensitivity of our assay that has the best detection limit to inorganic pro-oxidants compared to other oxidative-stress sensitive bioreporters in the literature. The bioreporter detected pro-oxidants in environmental samples. The assay has a reasonable sensitivity, however, it still lacks sensitivity to detect pro-oxidants at concentrations lower than those shown to be toxic to many aquatic species. Within-lab reproducibility and robustness were determined to be acceptable. For stress-specific bioreporters to be incorporated in regulative legislations and industrial monitoring programs there is a need to improve the sensitivity of these assays, they need to be calibrated with other relevant pro-oxidants, inter-lab reproducibility needs to be established and robustness to environmental samples needs to be further tested. To further validate the sensitivity and ecotoxicological relevance of the bioreporter as a relevant predictive tool, stress-specific bioreporter assays need to be performed in parallel with traditional ecotoxicological assays using contaminated environmental samples.
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Hsu, Kuei-Ling C. "Variability of two sampling methods in plaque samples." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2008m/hsu.pdf.

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Galada, Ncebakazi. "Metagenomic analysis and characterization of microbial diversity from hydrothermal samples of El Tatio geyser field, Chile." Thesis, University of the Western Cape, 2012. http://hdl.handle.net/11394/4014.

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Philosophiae Doctor - PhD
The El Tatio geyser field (ETGF) is the largest known geothermal field in Chile, forming part of a wide spectrum of extremophilic habitats in the country. The ETGF is NaCl rich, with high concentrations of toxic elements such as Li, As and Cs, which are contributed mainly by volcanic activities in the region. Most previous studies in the area have focused on the geology and geochemistry for mining purposes, as well as on the search for geothermal resources for power generation. Very little is currently known about the composition of the microbial communities of the ETGF, which makes the study reported here of particular novelty.A metagenomic approach, involving the amplification of 16S rRNA gene phylogenetic markers from metagenomic DNA was used to investigate seven different sites within the geyser field. The sample sites were characterized by high temperatures (80-85 °C) and a range of pH values (6.3-8). Various molecular methods, including clone library construction and PCR-DGGE analyses were used to target a wide range of microbial populations within the ETGF sites. Multivariate analysis was also applied to assess differences in the microbial diversity from different sites and to correlate microbial diversity with environmental conditions. Culture-dependent screening of novel nanoarchaeal species was also undertaken.These were coupled with PCR and other detection methods such as fluorescent in situ hybridization (FISH) to trace the presence of nanoarchaeal signals from enriched cultures.The results have shown that the ETGF encompasses a limited microbial diversity represented by only 30 dominant phylotypes, and most likely due to the toxic chemical content of the geyser field. The microbial representatives identified were assigned to OTUs from archaeal,nanoarchaeal and bacterial taxonomic groups. The dominant microbial taxa included members of the Proteobacteria, Firmicutes, Aquificae, Actinobacteria, Euryarchaeota(Halobacteriales, Archaeoglobales), Crenarchaeota (Thermoproteales, Desulfurococcales),together with uncultured representatives of the bacteria, archaea and nanoarchaeota. Notably,representatives of mesophilic, thermophilic and hyperthermophilic taxonomic groups were all detected in ETGF samples. This is attributed to various factors such as temperature gradients and dispersal mechanisms (e.g. natural forces such as rain and volcanic activities). Principal component analysis (PCA) showed significant differences (P < 0.05) in the microbial diversity of the ETGF samples, with principal components (based on the sequenced species from both 16S rRNA clone libraries and PCR-DGGE profiles) explaining up to 62.7% of variance. Furthermore, CCA showed that the differences in phylogenetic diversity were most influenced by temperature and salinity. This was also confirmed by the sequencing results,which showed that hyperthermophilic and haloarchaeal taxa were dominant in the ETGF sites. However, conductivity and pH were also found to contribute to variations in the microbial diversity of the experimental samples, with TDS (total dissolved solids) being a less influential factor. Attempts to generate nanoarchaeal-host co-cultures, and to recover sufficient nanoarchaeal genomic DNA for fosmid and/or large insert cloning for comparative genome analysis, were unsuccessful.This study is the first to employ metagenomic approaches to analyse the microbial diversity of sites in the ETGF, and has expanded our knowledge of microbiota present in this geyser field.
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Moreno, Lilliana I. "The Effect of Sample and Sample Matrix on DNA Processing: Mechanisms for the Detection and Management of Inhibition in Forensic Samples." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/1764.

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The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.
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He, Jizheng, and n/a. "Molecular Biological Studies of Soil Microbial Communities Under Different Management Practices in Forest Ecosystems of Queensland." Griffith University. Australian School of Environmental Studies, 2005. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20060309.095702.

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Soil microorganisms play important roles in maintaining soil quality and ecosystem health. Development of effective methods for studying the composition, diversity, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil quality. Forest management strategies and practices are of vital significance for sustainable forest production. How the different forest management measures will influence soil microbial communities is a widespread concern of forest industry and scientific communities. Only a small proportion (~0.1%) of the bacteria from natural habitats can be cultured on laboratory growth media. Direct extraction of whole-community DNA from soil, followed by polymerase chain reaction (PCR) and other analysis circumvents the problems of the culture-dependent methods and may shed light on a broader range of microbial communities in the soil. DNA-based molecular methods rely on high quality soil microbial DNA as template, and thus extraction of good quality DNA from soil samples has been a challenge because of the complex and heterogeneous nature of the soil matrix. The objectives of this research were to establish a set of DNA-based molecular methods and to apply them to investigate forest soil microbial composition and diversity. Soil samples were collected from different forest ecosystems, i.e., the natural forest (YNF) and the first rotation (~ 50 years) (Y1R) and the second rotation (~ 1 year) (Y2R) of hoop pine plantations at Yarraman, and from different forest residue management practices (the experiments had established 6.4 years before the samples were collected) at Gympie, two long-term experimental sites of the Queensland Department of Primary Industry-Forestry in subtropical Queensland, Australia. Some DNA-based molecular techniques, including DNA extraction and purification, PCR amplification, DNA screening, cloning, sequencing and phylogenetic analyses, were explored using Yarraman soil samples, which were high in organic matter, clay and iron oxide contents. A set of methods was assembled based on the recommendations of the method development experiments and applied to the investigations of the microbial composition and diversity of the Yarraman and Gympie soil samples. Four soil DNA extraction methods, including the Zhou method (Zhou et al., 1996), the Holben method (Holben, 1994), the UltraClean (Mo Bio) and FastDNA (Bio 101) soil DNA extraction kits, were explored. It was necessary to modify these methods for Yarraman soil. I designed and introduced a pre-lysis buffer washing step, to partially remove soil humic substances and promote soil dispersion. This modification greatly improved the quality of the extracted DNA, decreasing co-extracted humic substances by 31% and increasing DNA yield by 24%. The improved Holben method was recommended for fungal community studies, and the improved Zhou method for bacterial community studies. The extracted DNA was good in quality, with a consistent size of ~20 kb and a yield of 48-87 g g-1 soil, and could be successfully used for 16S (Zhou method) and 18S (Holben method) rDNA amplifications. For less difficult environmental samples, UltraClean kits could be a good option, because they are simple and fast and the extracted DNA are also of good quality. Screening of the DNA PCR products using TGGE, Heteroduplex-TGGE and SSCP was also explored. These methods were not so effective for the screening of the soil DNA PCR products, owing to the difficulty in interpretation of the results. Cloning was a necessary step to obtain a single sequence at species level in soil microbial community studies. The screening of the clone library by TGGE, Heteroduplex-TGGE and SSCP could only separate the clones into several major bands, although SSCP gave better separation. Sequencing of selected clones directly from the clone library obtained ultimate results of microbial taxonomic composition and diversity through well-established sequence analysis software packages and the databases. It was recommended that, in this project with the target of microbial community composition and diversity, soil DNA PCR products were directly cloned to construct clone libraries and a sample of clones were sequenced to achieve an estimate of the taxonomic composition of the soil. Fungal communities of the Yarraman soil samples under the natural forest (YNF) and the hoop pine plantations (YHP) were investigated using 18S rDNA based cloning and sequencing approaches. Twenty-eight clone sequences were obtained and analysed. Three fungal orders, i.e., Zygomycota, Ascomycota and Basidiomycota were detected from the YNF and YHP samples. By contrast, culture-based analyses of fungi in the literature were mostly Ascomycetes. YNF appeared to have more Ascomycota but less Zygomycota than YHP, and within the Zygomycota order, YHP had more unidentified species than YNF. Bacterial communities of Yarraman soil samples of YNF, Y1R and Y2R were investigated using 16S rDNA-based cloning and sequencing approaches. 305 16S rDNA clone sequences were analysed and showed an overall bacterial community composition of Unclassified bacteria (34.4%), Proteobacteria (22.0%), Verrucomicrobia (15.7%), Acidobacteria (10.2%), Chloroflexi (6.9%), Gemmatimonadetes (5.6%), and Actinobacteria (5.2%). There was a significant difference among YNF, Y1R and Y2R in the taxonomic group composition. YNF had a greater proportion of Acidobacteria (18.0%), Verrucomicrobia (23.0%) and Chloroflexi (9.0%) than Y1R and Y2R (corresponding to 6.3%, 12.1% and 5.9%, respectively), while Y1R and Y2R had a higher percentage of the Unclassified group (38.5% for Y1R and 46.5% for Y2R) than YNF (18.0%). For the Proteobacteria group, YNF had more Alpha-subdivision but Y1R and Y2R had more Delta-subdivision. From YNF to Y1R to Y2R, the clone sequence variable site ratios, 5% and 10% OTU numbers and Shannon's diversity index H' values tended to decrease, indicating the soil bacterial diversity decreased from the natural forest to the first and the second rotation hoop pine plantations. The large amount of unclassified clone sequences could imply a novel group of bacteria in the soil, particularly in the hoop pine soil samples. Alternatively they may result from artefacts during the PCR process. Bacterial communities of the Gympie soil under different residue management practices, i.e., residue (litter plus logging residue) removed (G0R), residue retained (G1R), and residue doubled (G2R), were also investigated using the 16S rDNA-based cloning and sequencing approaches. Acidobacteria (37.6%) and Proteobacteria (35.6%, including Alpha-subdivision of 29.9% and Gamma-subdivision of 5.7%) were dominant components of the communities, followed by Actinobacteria (14.7%), Verrucomicrobia (7.3%) and Unclassified bacteria. There was no significant difference among G0R, G1R and G2R in the bacterial community compositions and diversity. These findings provided an in-depth vision of the soil microbial communities under different forest management practices. Their combination with other soil analysis results, such as physical and chemical properties, and forest production data, could provide an improved understanding of sustainable forest management strategies.
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Radtke, Kristin. "Microbial biodiversity in permafrost and ground ice samples and survival of High Arctic isolate Cryptococcus NP33 under simulated Martian conditions." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103609.

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The work in this thesis consisted of two studies: 1) analysis of the microbial biodiversity of multiple ground ice types from the Arctic and the High Arctic; 2)examination of the survival of Cryptococcus NP33 under simulated Martian conditions over 41 days. The first study involved culture-dependent and independent evaluations of the microbial communities found in a buried firnified snow bank, a buried glacier, a pingo and ice wedges. Direct and culturable counts in the various ground ice types differed from each other (104 – 108 cellsmL-1 direct counts; 0 - 105 CFUmL-1 culturable counts), and were only weakly correlated to increasing sample age. Culturable counts were consistently highest in ice wedge samples. All sample isolates were dominated by Actinobacteria. Bacterial pyrosequencing analysis for one ice wedge showed a dominance (<50% of sequences) by Gammaproteobacteria. In an Archaeal clone library of the buried glacier, no clones were closely related to sequenced isolates, but were similar (>90%) to uncharacterized clones from marine environments. The pingo Bacterial clone library clones matched closely to environmental isolates as well as clones from cryoenvironments as well as soil environments. For the survivability study, Cryptotoccus strain NP33 was selected as a candidate organism to undergo Martian simulations. After 41 simulation days, it had a half-life of 10.1 days in simulated sunlightand 16.1 days in darkness. The compiled results suggest that the organism traits most crucial to survival under simulated Martian conditions were desiccation, radiation and freeze-thaw resistance.
Cette thèse contient deux études : 1) la biodiversité de différents types de glacesde sol de l'Arctique et du Grand Arctique, de même que la survie de Cryptococcus NP33dans des conditions martiennes simulées pendant 41 jours. La première étude impliquait des analyses dépendantes et indépendantes des conditions de culture pour évaluer les communautés microbiennes dans une congère névée enterrée, un glacier enterré, un pingo et des coins de glace. Les nombres de cellules totales et les nombres de cellules culturées dans les différents types de glaces de sol variaient (104 – 108 cellulesmL-1 nombre total; 0- 105 CFUmL-1 cellules culturées), et étaient que très faiblement dépendants de l'âge du iispécimen. Les nombres de cellules culturées étaient constamment plus élevées dans les coins de glace. Actinobacteria dominait les isolats de chaque spécimen. Un pyroséquençage bactérien d'un coin de glace a révélé une dominance (>50% desséquences) de Gammaproteobacteria. Dans une librairie de clones d'Archées du glacier enterré, les clones avaient peu de similarité à des isolats environnementaux, mais étaient similaires (>90%) à des clones environnementaux non-caractérisés d'environnements marins. Dans une librairie de clones de Bactéries du pingo, les clones étaient très similaires à des isolats et des clones provenant de cryo-environnements et d'environnements de sol. Pour la simulation martienne, Cryptococcus NP33 a été choisicomme organisme candidat suite à des expériments pour sélectionner des organismes résistant à la dessiccation, au froid et aux concentrations élevées de sel. Au cours de 41 jours dans le simulateur, Cryptococcus NP33 avait une demi-vie de 10.1 jours dans le soleil simulé et 16.1 jours dans le noir. Halorubrum avait un taux de survie de 100%(demi-vie estimée de ~70 - ∞ jours), tandis que d'autres organismes avaient une demi-vie beaucoup moins élevée (~2 - ~8 jours). Les résultats combinés suggèrent que les caractéristiques nécessaires à la survie dans des conditions martiennes simulées étaient la résistance à la dessiccation, la radiation et aux cycles de gel-dégel.
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Keeley, Ryan F. "Design and Implementation of Degenerate qPCR/qRT-PCR Primers to Detect Microbial Nitrogen Metabolism in Wastewater and Wastewater-Related Samples." Scholar Commons, 2019. https://scholarcommons.usf.edu/etd/7826.

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Nitrogen cycling processes can be tracked using quantitative Polymerase Chain Reaction (qPCR) to determine the presence and qReverse Transcriptase-PCR (qRT-PCR) to determine expression of key genes, or ‘biological markers’, for nitrogen metabolism. Nitrification is catalyzed in part, by two enzymes: ammonia monooxygenase (AMO; NH3 NH2OH) and nitrite oxidoreductase (NXR; NO2- NO3-). For denitrification, four enzymes act sequentially: nitrate reductase (NAR/NAP; NO3- NO2-), nitrite reductase (NIR; NO2- NO), nitric oxide reductase (NOR; NO  N2O), and nitrous oxide reductase (NOS; N2O  N2). A principle of wastewater treatment (WWT) is to remove excess nitrogen by taking advantage of natural nitrogen cycling or biological nitrogen removal (BNR). This process involves using microorganisms to bring influent ammonia through nitrification and denitrification to release nitrogen gas, which does not contribute to eutrophication. A novel shortcut nitrogen removal configuration could increase nitrogen removal efficiency by promoting nitritation/denitritation, reducing the classic nitrogen cycle by removing the redundant oxidation/reduction step to nitrate (NO3-). Here, three nitrogen transformations were used to track the three main phases in the nitrogen cycle; ammonia monooxygenase for nitrification, nitrite oxidoreductase for shortcut, and nitrous oxide reductase for denitrification. Primers for qPCR and qRT-PCR were designed to capture as much sequence diversity as possible for each step. Genes from bacteria known to perform the nitrogen transformations of interest (amoA, nxrB, nosZ) were used to BLAST-query the Integrated Microbial Genomes & Microbiomes database (img.jgi.doe.gov) to find homologs from organisms commonly found in WWT. These sequences were then aligned to find regions sufficiently conserved for primer design. These PCR primers were tested against standards for each gene and used to track nitrogen transformation potential and expression in a novel lab-scale algal photo-sequencing batch reactor which promotes shortcut nitrogen removal from wastewater across three solids retention times (SRT, or mean cell residence time); 5, 10 and 15 days. SRT 15 had the greatest total nitrogen removal with nitritation and denitritation observed. Nitrate was not detected in the first cycle and shortcut nitrogen removal was supported by low levels of nxrB genes and transcripts. Simultaneous nitrification/denitrification was supported by elevated concentrations of nosZ during the light period and less nitrite produced than ammonium consumed. Nitritation was predominantly performed by Betaproteobacteria amoA and nitrous oxide reduction was predominantly from nosZ group I (Proteobacteria-type).
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Zu, Theresah Nom Korbieh. "Phenotypic and Metabolic Profiling of Biological Samples in Near Real-Time Using Raman Spectroscopy." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/65153.

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Raman spectroscopy, together with multivariate statistical analyses, has proven to be a near real-time analytical technique capable of phenotyping cells, tissues and organs. This dissertation will show exclusively the application of the Raman spectroscopy phenotypic profiling method to; (i) microbial toxicity, (ii) ex-vivo organ perfusion, and (iii) subcellular location targeting. Real-time analytical methods for monitoring living biological systems will enable study of the physiological changes associated with growth, genetic manipulations, and adverse environmental conditions. Most existing analytical methods (NMR exempt), though highly accurate, must be performed off-line and most require destruction of the studied sample. These attributes make these methodologies less desirable to the study of physiological changes of cells, tissues, and organs. In this work, Raman spectroscopy has been identified and shown to be a good candidate for real-time analysis mainly because it can be performed: (i) in near real-time, (ii) non-destructively and with minimal sample preparation, (iii) through a glass barrier (i.e., can be performed in situ), and (iv) with minimal spectral interference from water. Here, Raman spectroscopy was used in combination with multivariate statistics to analyze the differing toxic effects of 4-C chain alcohols on E. coli. Good correlations were established between Raman spectra and off-line analytical techniques used to measure: (i) saturated, unsaturated, and cyclopropane fatty acids; (ii) amino acid composition of total protein; and (iii) cell membrane fluidity. Also, Raman 'fingerprint' analysis was used to discriminate among different phenotypic responses of cells. In addition, this methodology was applied to analyze perfusates of organs maintained by the VasoWave® organ perfusion system. Raman fingerprints can be used to assess organ health, and it is believed this data can be used to inform decisions such as whether or not to transplant an organ. Finally, molecular biology techniques were used to design and produce specific protein targets harboring a silver binding domain fusion, which upon release migrate to specific subcellular locations. By employing the related technique of surface-enhanced Raman scattering (SERS), which produces a highly amplified Raman signal in the presence of metallic nanoparticle substrates (e.g., silver nanoparticles), different regions of the E. coli cell structure were studied. The target regions studied by the technique included: (i) outer cell membrane, (ii) periplasm, and the (iii) cytoplasm.
Ph. D.
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Books on the topic "Microbial samples"

1

Roche, Karen. Genotype Detection In Environmental Samples. Dublin: University College Dublin, 1998.

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Vogel, J. R. Microbe concentrations, laser particle counts, and stable hydrogen and oxygen isotope ratios in samples from a riverbank filtration study, Platte River, Nebraska, 2002 to 2004. Reston, Va: U.S. Geological Survey, 2005.

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Mars, Sample Handling Protocol Workshop Series (2001 San Diego Calif ). Mars sample handling protocol workshop series: Interim report of the workshop series, Workshop 3 proceedings and final report, San Diego, California, March 19-21, 2001. Moffett Field, Calif: National Aeronautics and Space Administration, Ames Research Center, 2001.

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National Research Council (U.S.). Space Studies Board, National Research Council (U.S.). Division on Engineering and Physical Sciences, and National Academies Press (U.S.), eds. Assessment of planetary protection requirements for Mars sample return missions. Washington, D.C: National Academies Press, 2009.

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Mars sample handling protocol workshop series: Interim report of the workshop series Workshop 1 proceedings and final report, Bethesda, Maryland, March 20-22, 2000. Moffett Field, Calif: National Aeronautics and Space Administration, Ames Research Center, 2000.

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Mars sample handling protocol workshop series: Interim report of the workshop series Workshop 1 proceedings and final report, Bethesda, Maryland, March 20-22, 2000. Moffett Field, Calif: National Aeronautics and Space Administration, Ames Research Center, 2000.

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Mars sample handling protocol workshop series: Interim report of the workshop series, Workshop 3 proceedings and final report, San Diego, California, March 19-21, 2001. Moffett Field, Calif: National Aeronautics and Space Administration, Ames Research Center, 2001.

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S, Race Margaret, Rummel J. D, and Ames Research Center, eds. Mars sample handling protocol workshop series: Interim report of the workshop series Workshop 1 proceedings and final report, Bethesda, Maryland, March 20-22, 2000. Moffett Field, Calif: National Aeronautics and Space Administration, Ames Research Center, 2000.

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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Some early landmark studies. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0011.

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Chapter 11 entitled “Some early landmark studies” revisits several seminal articles that paved the way for the field of eDNA research. It first evokes the paper that first coined the expression “environmental DNA” in the late 1980s. Then, it describes how eDNA was first exploited in the early 1990s to reveal an unsuspected microbial diversity that morphology- or cultivation-based methods had failed to reach. In the late 1990s, microbiologists began to explore in several pioneer papers the functional insight provided by “metagenomes” (i.e., the collective genomes found in eDNA samples). In the 2000s, eDNA analysis was finally extended to macroorganisms. Chapter 11 reports such a use in two very different contexts (i.e., the detection of a contemporary invasive species, the bullfrog, and the reconstruction of past plant and animal communities from sediment and permafrost samples).
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L, Lewis David, and United States. Environmental Protection Agency., eds. Treating soil solution samplers to prevent microbial removal of analytes. [Washington, D.C.?: U.S. Environmental Protection Agency, 1992.

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Book chapters on the topic "Microbial samples"

1

Jansson, Janet K., and Thomas Leser. "Quantitative PCR of environmental samples." In Molecular Microbial Ecology Manual, 43–61. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0215-2_5.

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Insam, Heribert. "A New Set of Substrates Proposed for Community Characterization in Environmental Samples." In Microbial Communities, 259–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60694-6_25.

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van Verseveld, Henk W., Wilfred F. M. Röling, Diman van Rossum, Anniet M. Laverman, Stef van Dijck, Martin Braster, and Fred C. Boogerd. "Phenetic and Genetic Analyses of Bacterial Populations in Fermented Food and Environmental Samples." In Microbial Communities, 19–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60694-6_3.

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Delaney, Sarah, Richard Murphy, and Fiona Walsh. "Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples." In Microbial Transposon Mutagenesis, 151–57. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9570-7_14.

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Jansson, Janet K., and Thomas Leser. "Section 2 update: Quantitative PCR of environmental samples." In Molecular Microbial Ecology Manual, 2347–65. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-2177-0_213.

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Akaihe, Chidinma Lynda, Ebubechukwu Nnamdi Dim, Chizoba I. Ezugwu, Emeka Innocent Nweze, and Paul Ekene Chidebelu. "Analytical Techniques/Technologies for Studying Ecological Microbial Samples." In Environmental and Microbial Biotechnology, 481–517. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-15-8999-7_18.

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McHardy, Alice Carolyn, and Kaustubh Patil. "Phylogenetic Binning of Metagenome Sequence Samples." In Handbook of Molecular Microbial Ecology I, 353–58. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010518.ch40.

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Rimbara, Emiko, Masanori Sasatsu, and David Y. Graham. "PCR Detection of Helicobacter pylori in Clinical Samples." In PCR Detection of Microbial Pathogens, 279–87. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-60327-353-4_19.

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Ansari, A. Thaminum. "Biosorption and Discolorization of Textile Dye Effluent Using Fungi Isolated From Soil Samples Collected Near Textile Dye Industry." In Microbial Biofilms, 271–94. Boca Raton : CRC Press, 2020.: CRC Press, 2020. http://dx.doi.org/10.1201/9780367415075-17.

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Lavender, Caroline J., and Janet A. M. Fyfe. "Direct Detection of Mycobacterium ulcerans in Clinical Specimens and Environmental Samples." In PCR Detection of Microbial Pathogens, 201–16. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-60327-353-4_13.

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Conference papers on the topic "Microbial samples"

1

Sulaiman, I., B. Wu, J. C. Tsay, Y. Li, M. Sauthoff, A. S. Scott, K. Gershner, et al. "Functional Microbiomic Approaches Using Lower Airway Samples Identify a Subset of Lung Microbial Communities with Evidence of Active Microbial Metabolism." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4246.

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Xu, Zhaohui, Pooja Yadav, Zhizhou Zhang, Sankardas Roy, and Huimin Zhang. "Quantification of microbial species in solid state fermentation samples using signature genomic sequences." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217781.

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Chebotar, V. K., A. N. Zaplatkin, O. V. Komarova, M. E. Baganova, N. I. Polukhin, and S. V. Balakina. "Microbial preparations on the basis of endophytic bacteria for nutrition and protection of potatoes from diseases." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.051.

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The microbiome of cultivated and wild potato species was studied, effective endophytic bacteria were isolated, and experimental samples of microbial preparations were developed. The effectiveness of microbial preparations based on Bacillus thuringiensis W65 and Paenibacillus xylanexedens N40 strains in the Leningrad and Novosibirsk regions on new potato varieties is shown.
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Garcia, Alfonso, Trevor Place, Michael Holm, Jennifer Sargent, and Andrew Oliver. "Pipeline Sludge Sampling for Assessing Internal Corrosion Threat." In 2014 10th International Pipeline Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/ipc2014-33113.

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Internal corrosion sometimes occurs under deposits of solid particles on the bottom of transmission pipelines. The solids trap water with soluble products and other nutrients which can support the development of microbial communities and may lead to Microbiologically Influenced Corrosion (MIC). Corrosion processes associated with the metabolic activities of specific bacteria have been discussed elsewhere, but the simple presence of large microbial populations may increase the risk of internal corrosion owing to the ability of biofilms to extract and concentrate water at the pipe floor. As a method to monitor the internal corrosion threat in transmission pipelines and recommend mitigating activities for corrosion management, reliable microbial content and corrosion activity correlations are desired. Sludge samples have been obtained from cleaning pigs at the pipe trap and analyzed using Biological Activity Reaction Test (BART™) (or serial dilution test), Dean-Stark analysis, XRD and EDX. These tests provide information about certain bacterial populations, water / solid / hydrocarbon content, and crystalline/elemental composition of these solids, respectively. Despite best efforts, bacterial population/activity of pipeline sludge samples exhibit high variability and are difficult to correlate to actual internal corrosion in a pipeline. Considering that bacterial populations in pipeline sludge may be a meaningful representation of the internal corrosion threat to a transmission pipeline, a more rigorous approach on the sludge sampling procedure is necessary to improve the accuracy and reliability of the bacterial assays. It is also important to control such variables as storage temperature of the samples, exposure to air, and storage duration prior to enumeration — as these may affect the viability of the sample and enumeration results. This report presents historical pipeline sludge analysis data and suggests a method to evaluate data containing high variability. Practical recommendations to reduce data variability through handling and storage of sludge samples are also discussed.
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Jadhav, P., S. Ashokkumar, and N. Nagwekar. "Microbial load reduction using modified Solar Conduction Dryer with composite filters." In 21st International Drying Symposium. Valencia: Universitat Politècnica València, 2018. http://dx.doi.org/10.4995/ids2018.2018.7728.

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The present work studies the microbial load reduction in sapota and beet root by three different drying methods i.e. Open Sun Drying (OSD), Solar Conduction Drying (SCD) and a modified SCD with filters (SCDF). Parameters analyzed were water activity, moisture content, drying kinetics, Total Viable Counts, Total Fungal Counts and ash content. It was found that the samples dried in SCDF showed least microbial counts, faster drying times and lower ash content as comparison to OSD. This study shows that SCD and its modification provide a better alternative for low cost drying of fruits and vegetables for quality retention. Keywords: Microbial reduction; SCD Filters; Sapota; Beetroot
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Zhang, Chao, Prashant Vijay Thakkar, Felice Schnoll-Sussman, Bridget McClure, Michelle Bigg, Greg Sonnenberg, Doron Betel, and Manish Shah. "Abstract A04: Microbial and immunologic characterization of gastroesophageal tissue biopsy samples: A multiparametric analysis." In Abstracts: AACR Special Conference on Tumor Immunology and Immunotherapy; October 1-4, 2017; Boston, MA. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/2326-6074.tumimm17-a04.

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Bangham, Madeleine, and Katherine Myall. "Investigating microbial communities in interstitial lung disease by standard culture of bronchioalveolar lavage samples." In ERS International Congress 2018 abstracts. European Respiratory Society, 2018. http://dx.doi.org/10.1183/13993003.congress-2018.pa2960.

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Rahman, Jessica S., Jinyan Li, Juanying Xie, Shoshana Fogelman, and Michael Blumenstein. "Connectivity Based Method for Clustering Microbial Communities from Metagenomics Data of Water and Soil Samples." In 2018 International Joint Conference on Neural Networks (IJCNN). IEEE, 2018. http://dx.doi.org/10.1109/ijcnn.2018.8489220.

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Lu, Jia, Xiaohou Shao, Chao Yin, Xinyu Mao, Long Wang, Yong Min, and Muchen Shu. "Preliminary study on removal of nitrate nitrogen in aqueous samples by microbial nano-silica ball." In International conference on Human Health and Medical Engineering. Southampton, UK: WIT Press, 2014. http://dx.doi.org/10.2495/hhme131442.

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Kublanovskaya, A. A., P. A. Zaytsev, K. A. Chekanov, T. A. Fedorenko, S. G. Vasilieva, A. E. Solovchenko, and E. S. Lobakova. "Comparative analysis of microbial communities from phosphorus-polluted sites from Northern (Russia) and Southern (Israel) latitudes." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.136.

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The biodiversity of microbial communities from phosphorus-polluted sites from Northern and Southern regions was investigated, groups of microorganisms with biotechnological potential were detected. According to the results, samples from Southern regions were characterized by lower biodiversity than the northern ones.
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Reports on the topic "Microbial samples"

1

Swanson, Juliet S. Microbial Characterization of Halite and Groundwater Samples from the WIPP. Office of Scientific and Technical Information (OSTI), August 2013. http://dx.doi.org/10.2172/1089877.

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Berry, C. J., C. B. Fliermans, and J. Santo Domingo. Microbial Condition of Water Samples from Foreign Fuel Storage Facilities. Office of Scientific and Technical Information (OSTI), October 1997. http://dx.doi.org/10.2172/630875.

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Swanson, Juliet S., Donald T. Reed, David A. Ams, Diana Norden, and Karen A. Simmons. Status Report on the Microbial Characterization of Halite and Groundwater Samples from the WIPP. Office of Scientific and Technical Information (OSTI), July 2012. http://dx.doi.org/10.2172/1045985.

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Laurinavichius, K. S. Experimental Investigation of Microbially Induced Corrosion of Test Samples and Effect of Self-Assembled Hydrophobic Monolayers. Exposure of Test Samples to Continuous Microbial Cultures, Chemical Analysis, and Biochemical Studies. Office of Scientific and Technical Information (OSTI), September 1998. http://dx.doi.org/10.2172/758748.

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Thurston, Alison, Zoe Courville, Lauren Farnsworth, Ross Lieblappen, Shelby Rosten, John Fegyveresi, Stacy Doherty, Robert Jones, and Robyn Barbato. Microscale dynamics between dust and microorganisms in alpine snowpack. Engineer Research and Development Center (U.S.), March 2021. http://dx.doi.org/10.21079/11681/40079.

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Dust particles carry microbial and chemical signatures from source regions to deposition regions. Dust and its occupying microorganisms are incorporated into, and can alter, snowpack physical properties including snow structure and resultant radiative and mechanical properties that in turn affect larger-scale properties, including surrounding hydrology and maneuverability. Microorganisms attached to deposited dust maintain genetic evidence of source substrates and can be potentially used as bio-sensors. The objective of this study was to investigate the impact of dust-associated microbial deposition on snowpack and microstructure. As part of this effort, we characterized the microbial communities deposited through dust transport, examined dust provenance, and identified the microscale location and fate of dust within a changing snow matrix. We found dust characteristics varied with deposition event and that dust particles were generally embedded in the snow grains, with a small fraction of the dust particles residing on the exterior of the snow matrix. Dust deposition appears to retard expected late season snow grain growth. Both bacteria and fungi were identified in the collected snow samples.
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