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Dna extraction soil

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https://www.readbyqxmd.com/read/29346412/a-comparative-analysis-of-preservation-techniques-for-the-optimal-molecular-detection-of-hookworm-dna-in-a-human-fecal-specimen
#1
Marina Papaiakovou, Nils Pilotte, Ben Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabian Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A Williams
BACKGROUND: Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29342372/enrichment-of-antibiotic-resistance-genes-in-soil-receiving-composts-derived-from-swine-manure-yard-wastes-or-food-wastes-and-evidence-for-multi-year-persistence-of-swine-i-i-clostridium-i-i-spp
#2
Andrew Scott, Yuan-Ching Tien, Craig F Drury, W Daniel Reynolds, Edward Topp
The impact of amendment with swine manure composts (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared to untreated control soil, all three amendment types increased the abundance of gene targets for up to four years post-application...
January 17, 2018: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#3
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29319522/characterization-of-microbial-communities-in-acidified-sulfur-containing-soils
#4
Grzegorz Czerwonka, Iwona Konieczna, Paulina Żarnowiec, Artur Zieliński, Agnieszka Malinowska-Gniewosz, Agnieszka Gałuszka, Zdzisław Migaszewski, Wiesław Kaca
Over a period of three years, microbial communities in acidified soil with high sulfur content were analyzed. In soil water extracts ureolytic, proteolytic, oxidoreductive, and lipolytic activity were detected. The presented results indicate that the enzymatic activity of soil microbial communities varied considerably over time. Isolated 26 (80%) bacterial strains belonged to genus Bacillus sp. and were identified by cultivation and 16S rRNA methods. The commercially available procedures for bacterial DNA isolation from acidified soil failed, therefore a new, specific DNA isolation method was established...
December 4, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29302623/molecular-characterization-of-environmental-cladosporium-species-isolated-from-iran
#5
I Ghiaie Asl, M Motamedi, G R Shokuhi, N Jalalizand, A Farhang, H Mirhendi
Background and Purpose: Cladosporium species are ubiquitous, saprobic, dematiaceous fungi, only infrequently associated with human and animal opportunistic infections. Materials and Methods: Airborne samples were collected using the settle plate method, and soil samples were obtained from a depth of 5-10 cm of the superficial soil layer. Samples were cultured on Sabouraud dextrose agar (SDA) plates, incubated at 25°C, and examined daily for fungal colonies for two to three weeks...
March 2017: Advances in Medical Mycology (Iran)
https://www.readbyqxmd.com/read/29300934/effects-of-sample-preservation-and-dna-extraction-on-enumeration-of-antibiotic-resistance-genes-in-wastewater
#6
An-Dong Li, Jacob W Metch, Yulin Wang, Emily Garner, An Ni Zhang, Maria V Riquelme, Peter J Vikesland, Amy Pruden, Tong Zhang
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit, and ZR Fecal DNA MiniPrep™), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA...
December 27, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29285669/identification-of-metolachlor-mineralizing-bacteria-in-aerobic-and-anaerobic-soils-using-dna-stable-isotope-probing
#7
Ramdas G Kanissery, Allana Welsh, Andres Gomez, Lynn Connor, Gerald K Sims
The influence of soil environmental factors such as aeration on the ecology of microorganisms involved in the mineralization and degradation of the popular soil-applied pre-emergent herbicide, metolachlor is unknown. To address this knowledge gap, we utilized DNA-based stable isotope probing (SIP) where soil microcosms were incubated aerobically or anaerobically and received herbicide treatments with unlabeled metolachlor or 13C-metolachlor. Mineralization of metolachlor was confirmed as noted from the evolution of 14CO2 from 14C-metolachlor-treated microcosms and clearly demonstrated the efficient utilization of the herbicide as a carbon source...
December 28, 2017: Biodegradation
https://www.readbyqxmd.com/read/29281808/evaluation-of-the-novel-crassphage-marker-for-sewage-pollution-tracking-in-storm-drain-outfalls-in-tampa-florida
#8
Warish Ahmed, Aldo Lobos, Jacob Senkbeil, Jayme Peraud, Javier Gallard, Valerie J Harwood
CrAssphage are recently-discovered DNA bacteriophages that are prevalent and abundant in human feces and sewage. We assessed the performance characteristics of a crAssphage quantitative PCR (qPCR) assay for quantifying sewage impacts in stormwater and surface water in subtropical Tampa, Florida. The mean concentrations of crAssphage in untreated sewage ranged from 9.08 to 9.98 log10 gene copies/L. Specificity was 0.927 against 83 non-human fecal reference samples and the sensitivity was 1.0. Cross-reactivity was observed in DNA extracted from soiled poultry litter but the concentrations were substantially lower than untreated sewage...
December 24, 2017: Water Research
https://www.readbyqxmd.com/read/29279831/optimal-dna-isolation-method-for-detection-of-nontuberculous-mycobacteria-by-polymerase-chain-reaction
#9
Samira Mohammadi, Bahram Nasr Esfahani, Sharareh Moghim, Hossein Mirhendi, Fatemeh Riyahi Zaniani, Hajieh Ghasemian Safaei, Hossein Fazeli, Mahshid Salehi
Background: Nontuberculous mycobacteria (NTM) are a group of opportunistic pathogens and these are widely dispersed in water and soil resources. Identification of mycobacteria isolates by conventional methods including biochemical tests, growth rates, colony pigmentation, and presence of acid-fast bacilli is widely used, but these methods are time-consuming, labor-intensive, and may sometimes remain inconclusive. Materials and Methods: The DNA was extracted from NTM cultures using CTAB, Chelex, Chelex + Nonidet P-40, FTA® Elute card, and boiling The quantity and quality of the DNA extracted via these methods were determined using UV-photometer at 260 and 280 nm, and polymerase chain reaction (PCR) amplification of the heat-shock protein 65 gene with serially diluted DNA samples...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/29209407/heavy-metals-effect-on-breast-cancer-progression
#10
А Romaniuk, M Lyndin, V Sikora, Y Lyndina, S Romaniuk, K Sikora
Background: Breast cancer is the most frequent localization of malignant process in American women and women of European countries. To date it is not possible to control the morbidity growth due to lack of effective ways of primary prevention. Comparing the incidence of breast cancer in developed countries with the countries of Asia and Africa, there is the fact of population predominance lesion in more urbanized countries. This suggests that the environment along with other factors, occupies a significant place in the initiation and progression of breast neoplasia...
2017: Journal of Occupational Medicine and Toxicology
https://www.readbyqxmd.com/read/29204941/temporal-dynamics-of-total-and-free-living-nitrogen-fixing-bacterial-community-abundance-and-structure-in-soil-with-and-without-history-of-arsenic-contamination-during-a-rice-growing-season
#11
Arindam Chakraborty, Ekramul Islam
Despite the fact that the nitrogen (N) fixers act as the key regulator of ecosystem process, a detailed study of their abundance, diversity, and dynamics in arsenic (As)-contaminated rice fields is missing so far. DNA extracted from soil followed by 16S rRNA and nifH gene-based real-time qPCR, clone library analysis, and DNA sequencing were used to examine the status of the total and diazotrophic communities in two agricultural fields with and without arsenic contamination history during one rice cultivation season...
December 5, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29184976/distinctive-soil-archaeal-communities-in-different-variants-of-tropical-equatorial-forest
#12
Dorsaf Kerfahi, Binu M Tripathi, J W Ferry Slik, Rahayu S Sukri, Salwana Jaafar, Jonathan M Adams
Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors...
November 29, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29178845/classification-of-a-new-phytoplasmas-subgroup-16srii-w-associated-with-crotalaria-witches-broom-diseases-in-oman-based-on-multigene-sequence-analysis
#13
Ali Al-Subhi, Saskia A Hogenhout, Rashid A Al-Yahyai, Abdullah M Al-Sadi
BACKGROUND: Crotalaria aegyptiaca, a low shrub is commonly observed in the sandy soils of wadis desert and is found throughout all regions in Oman. A survey for phytoplasma diseases was conducted. During a survey in a wild area in the northern regions of Oman in 2015, typical symptoms of phytoplasma infection were observed on C. aegyptiaca plants. The infected plants showed an excessive proliferation of their shoots and small leaves. RESULTS: The presence of phytoplasma in the phloem tissue of symptomatic C...
November 25, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/29118739/resolving-species-level-changes-in-a-representative-soil-bacterial-community-using-microfluidic-quantitative-pcr
#14
Hannah Kleyer, Robin Tecon, Dani Or
Rapid advances in genome sequencing technologies enable determination of relative bacterial abundances and community composition, yet, changes at the species level remain difficult to detect despite importance for certain ecological inferences. We present a method for extraction and direct quantification of species composition of a predefined multispecies bacterial community using microfluidic-based quantitative real-time PCR (qPCR). We employ a nested PCR approach based on universal 16S rRNA gene pre-amplification followed by detection and quantification of absolute abundance of bacterial species using microfluidic array of parallel singleplex qPCR reactions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29117585/metagenomics-profiling-for-assessing-microbial-diversity-in-both-active-and-closed-landfills
#15
Mohamad Yusof Zainun, Khanom Simarani
The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29106502/isolation-of-highly-thermostable-%C3%AE-xylosidases-from-a-hot-spring-soil-microbial-community-using-a-metagenomic-approach
#16
Masaru Sato, Migiwa Suda, Jiro Okuma, Tomohiko Kato, Yoshitsugu Hirose, Asuka Nishimura, Yasuhiko Kondo, Daisuke Shibata
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene...
August 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29104570/characterization-of-bacterial-and-fungal-community-dynamics-by-high-throughput-sequencing-hts-metabarcoding-during-flax-dew-retting
#17
Christophe Djemiel, Sébastien Grec, Simon Hawkins
Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS) DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq) on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29075440/efficient-isolation-method-for-high-quality-genomic-dna-from-cicada-exuviae
#18
Hoa Quynh Nguyen, Ye Inn Kim, Amaël Borzée, Yikweon Jang
In recent years, animal ethics issues have led researchers to explore nondestructive methods to access materials for genetic studies. Cicada exuviae are among those materials because they are cast skins that individuals left after molt and are easily collected. In this study, we aim to identify the most efficient extraction method to obtain high quantity and quality of DNA from cicada exuviae. We compared relative DNA yield and purity of six extraction protocols, including both manual protocols and available commercial kits, extracting from four different exoskeleton parts...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28959343/green-nanoparticles-engineering-on-root-knot-nematode-infecting-eggplants-and-their-effect-on-plant-dna-modification
#19
Kamal Fouad Abdellatif, Ragaa Hamouda Abdelfattah, Mostafa Sayed Mostafa El-Ansary
BACKGROUND: Root-knot nematodes are known to cause significant damage to eggplants. New approaches by green silver nanoparticles (GSN) are used to control plant-parasitic nematode to avoid chemical nematicide hazards. OBJECTIVES: Analyses of the incorporation of different concentrations of nanoparticles on two different algae (Ulva lactuca and Turbinaria turbinata) were carried out. Furethermore, the effect of GSN on the eggplant DNA profile was studied using RAPD and EST molecular markers...
December 2016: Iranian Journal of Biotechnology
https://www.readbyqxmd.com/read/28956398/-discovery-and-analysis-of-staphylococcus-aureus-biofilm-inhibitors-using-functional-metagenomics-approach
#20
Ying Zhu, Shumao Chai, Mingming Cao, Shaochen Wang, Zhiyang Feng
Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed "metagenomics". An E'mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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