keyword
MENU ▼
Read by QxMD icon Read
search

Dna extraction microbes

keyword
https://www.readbyqxmd.com/read/29677595/bioherbicides-current-knowledge-on-weed-control-mechanism
#1
REVIEW
Ramalingam Radhakrishnan, Abdulaziz A Alqarawi, Elsayed Fathi Abd Allah
Weed control is a challenging event during crop cultivation. Integrated management, including the application of bioherbicides, is an emerging method for weed control in sustainable agriculture. Plant extracts, allelochemicals and some microbes are utilized as bioherbicides to control weed populations. Bioherbicides based on plants and microbes inhibit the germination and growth of weeds; however,few studies conducted in weed physiology. This review ascribes the current knowledge of the physiological changes in weeds that occur during the exposure to bioherbicides...
April 17, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29667550/in-vitro-studies-on-cytotoxic-dna-protecting-antibiofilm-and-antibacterial-effects-of-biogenic-silver-nanoparticles-prepared-with-bergenia-ciliata-rhizome-extract
#2
Ghazna Zia, Haleema Sadia, Shabnam Nazir, Kiren Ejaz, Shaukat Ali, Ihsan-Ul-Haq, Tariq Iqbal, Muhammad Abdul Rauf Khan, Abida Raza, Saiqa Andleeb
BACKGROUND: Many health hazardous diseases are caused by clinical pathogens. Drug-resistant microbes are one of the major health problems in the world. To overcome the effect of infectious diseases new antimicrobial agent from nature has been explored which is environmentally friendly, less costly and more effective for the development of next-generation drugs. Bergenia ciliata and silver nitrate both have medicinal properties. OBJECTIVES: The aim of the current research was to evaluate the cytotoxic, and antibacterial effect of green synthesized nanoparticles using Bergenia ciliata rhizome against clinical bacterial pathogens...
April 17, 2018: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/29661230/a-comparison-of-methods-used-to-unveil-the-genetic-and-metabolic-pool-in-the-built-environment
#3
Cinta Gomez-Silvan, Marcus H Y Leung, Katherine A Grue, Randeep Kaur, Xinzhao Tong, Patrick K H Lee, Gary L Andersen
BACKGROUND: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs...
April 16, 2018: Microbiome
https://www.readbyqxmd.com/read/29651173/in-vitro-anticancer-activity-of-staphyloxanthin-pigment-extracted-from-staphylococcus-gallinarum-kx912244-a-gut-microbe-of-bombyx-mori
#4
Delicia Avilla Barretto, Shyam Kumar Vootla
The present study reports the in vitro biological nature of the pigment produced by Staphylococcus gallinarum KX912244, isolated as the gut microflora bacterium of the insect Bombyx mori . The purified pigment was characterized as Staphyloxanthin based on bio-physical characterization techniques like Fourier transform infrared spectroscopy, high performance liquid chromatography, Proton nuclear magnetic resonance spectroscopy (1 H NMR), Liquid chromatography-Mass spectroscopy and Gas chromatography-Mass spectroscopy...
June 2018: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/29630048/a-method-for-targeted-16s-sequencing-of-human-milk-samples
#5
Nicole H Tobin, Cora Woodward, Sara Zabih, David J Lee, Fan Li, Grace M Aldrovandi
Studies of microbial communities have become widespread with the development of relatively inexpensive, rapid, and high throughput sequencing. However, as with all these technologies, reproducible results depend on a laboratory workflow that incorporates appropriate precautions and controls. This is particularly important with low-biomass samples where contaminating bacterial DNA can generate misleading results. This article details a semi-automated workflow to identify microbes from human breast milk samples using targeted sequencing of the 16S ribosomal RNA (rRNA) V4 region on a low- to mid-throughput scale...
March 23, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29530467/tick-microbial-communities-within-enriched-extracts-of-amblyomma-maculatum
#6
A S Varela-Stokes, S H Park, J V Stokes, N A Gavron, S I Lee, G M Moraru, S C Ricke
Our objective of this study was to explore the bacterial microbiome in fresh or fresh-frozen adult Amblyomma maculatum (Gulf Coast ticks) using extracts enriched for microbial DNA. We collected 100 questing adult A. maculatum, surface disinfected them, and extracted DNA from individual ticks collected the same day or after storage at -80 °C. Because only extracts with microbial DNA concentrations above 2 ng/μL were considered suitable for individual analysis, we expected fewer samples to meet these requirements...
March 1, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29501294/human-beta-defensin-1-is-involved-in-the-susceptibility-to-adeno-tonsillar-hypertrophy
#7
Luisa Zupin, Fulvio Celsi, Martina Bresciani, Eva Orzan, Domenico Leonardo Grasso, Sergio Crovella
INTRODUCTION: Innate immunity molecules are known to play a pivotal role in the homeostasis of the oral mucosa, permitting the presence of commensal microflora and, at the same time, providing a first line of defense against pathogens attempting to invade the oral cavity. Tonsils represent the local immune tissue in oral cavity, being able to provide a non-specific response to pathogens; however, in the presence of microbes or foreign materials present in the mouth tonsils could became infected and develop chronic inflammation, thus leading to hypertrophy...
April 2018: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/29483941/genome-resolved-metagenomics-of-sugarcane-vinasse-bacteria
#8
Noriko A Cassman, Késia S Lourenço, Janaína B do Carmo, Heitor Cantarella, Eiko E Kuramae
Background: The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased N2 O emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29469169/alimentary-microbes-of-winter-form-drosophila-suzukii
#9
M T Fountain, J Bennett, M Cobo-Medina, R Conde Ruiz, G Deakin, A Delgado, R Harrison, N Harrison
Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA)...
February 22, 2018: Insect Molecular Biology
https://www.readbyqxmd.com/read/29433218/application-of-high-throughput-pyrosequencing-in-the-analysis-of-microbiota-of-food-commodities-procured-from-small-and-large-retail-outlets-in-a-u-s-metropolitan-area-a-pilot-study
#10
Daleniece Higgins, Chandan Pal, Irshad M Sulaiman, Chunrong Jia, Tyler Zerwekh, Scot E Dowd, Pratik Banerjee
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA...
March 2018: Food Research International
https://www.readbyqxmd.com/read/29361962/evaluation-of-biological-potential-of-selected-species-of-family-poaceae-from-bahawalpur-pakistan
#11
Iram Fatima, Sobia Kanwal, Tariq Mahmood
BACKGROUND: Oxidative stress as well as bacterial and fungal infections are common source of diseases while plants are source of medication for curative or protective purposes. Hence, aim of study was to compare the pharmacological potential of seven grass species in two different solvents i.e. ethanol and acetone. METHODS: Preliminary phytochemical tests were done and antioxidant activities were evaluated using ELISA and their IC50 values and AAI (%) were recorded...
January 24, 2018: BMC Complementary and Alternative Medicine
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
#12
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/29310749/culture-independent-approaches-to-chlamydial-genomics
#13
Alyce Taylor-Brown, Danielle Madden, Adam Polkinghorne
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement...
January 3, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29305057/comparison-of-dna-extraction-methods-for-human-gut-microbial-community-profiling
#14
Mi Young Lim, Eun-Ji Song, Sang Ho Kim, Jangwon Lee, Young-Do Nam
The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample...
March 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29295716/first-detection-and-genetic-characterisation-of-enterocytozoon-bieneusi-in-wild-deer-in-melbourne-s-water-catchments-in-australia
#15
Yan Zhang, Anson V Koehler, Tao Wang, Shane R Haydon, Robin B Gasser
BACKGROUND: Enterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, E. bieneusi has yet to be recorded in animals in Australia. Here, we undertook the first molecular epidemiological investigation of E. bieneusi in three species of deer (Cervus elaphus, Dama dama and Rusa unicolor) that live in the catchment areas that supply the city of Melbourne with drinking water. METHODS: Genomic DNA was extracted from a total of 610 individual faecal samples from wild deer, including sambar deer (Rusa unicolor) (n = 516), red deer (Cervus elaphus) (n = 77) and fallow deer (Dama dama) (n = 17) from nine catchment areas, and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ribosomal DNA as the genetic marker...
January 3, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29274973/short-communication-signs-of-host-genetic-regulation-in-the-microbiome-composition-in-2-dairy-breeds-holstein-and-brown-swiss
#16
O Gonzalez-Recio, I Zubiria, A García-Rodríguez, A Hurtado, R Atxaerandio
This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur (https://www.mothur.org/) in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database...
March 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29224074/sampling-extraction-and-high-throughput-sequencing-methods-for-environmental-microbial-and-viral-communities
#17
Pedro J Torres, Scott T Kelley
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29207565/delivery-mode-and-the-transition-of-pioneering-gut-microbiota-structure-composition-and-predicted-metabolic-function
#18
Noel T Mueller, Hakdong Shin, Aline Pizoni, Isabel C Werlang, Ursula Matte, Marcelo Z Goldani, Helena A S Goldani, Maria G Dominguez-Bello
Cesarean (C-section) delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium) hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool) 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges...
December 4, 2017: Genes
https://www.readbyqxmd.com/read/29161268/nucleic-acid-purification-from-plants-animals-and-microbes-in-under-30-seconds
#19
Yiping Zou, Michael Glenn Mason, Yuling Wang, Eugene Wee, Conny Turni, Patrick J Blackall, Matt Trau, Jose Ramon Botella
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed...
November 2017: PLoS Biology
https://www.readbyqxmd.com/read/29078799/comparing-microbiotas-in-the-upper-aerodigestive-and-lower-respiratory-tracts-of-lambs
#20
Laura Glendinning, David Collie, Steven Wright, Kenny M D Rutherford, Gerry McLachlan
BACKGROUND: Recently, the importance of the lung microbiota during health and disease has been examined in humans and in small animal models. Whilst sheep have been proposed as an appropriate large animal model for studying the pathophysiology of a number of important human respiratory diseases, it is clearly important to continually define the limits of agreement between these systems as new concepts emerge. In humans, it has recently been established that the lung microbiota is seeded by microbes from the oral cavity...
October 27, 2017: Microbiome
keyword
keyword
56892
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"