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Dna extraction grasses

Sofia Ghitarrini, Elisa Pierboni, Cristina Rondini, Emma Tedeschini, Gloria R Tovo, Giuseppe Frenguelli, Emidio Albertini
Grasses (Poaceae) are very common plants, which are widespread in all environments and urban areas. Despite their economical importance, they can represent a problem to humans due to their abundant production of allergenic pollen. Detailed information about the pollen season for these species is needed in order to plan adequate therapies and to warn allergic people about the risks they take in certain areas at certain moments. Moreover, precise identification of the causative species and their allergens is necessary when the patient is treated with allergen-specific immunotherapy...
April 2018: Ecology and Evolution
Jueeli D Vaidya, Bartholomeus van den Bogert, Joan E Edwards, Jos Boekhorst, Sanne van Gastelen, Edoardo Saccenti, Caroline M Plugge, Hauke Smidt
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100)...
2018: Frontiers in Microbiology
Cristina Saro, Eduarda Molina-Alcaide, Leticia Abecia, María José Ranilla, María Dolores Carro
The objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design...
April 2018: Archives of Animal Nutrition
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
Hisami Kobayashi, Takuya Nakasato, Mitsuo Sakamoto, Yoshihisa Ohtani, Fuminori Terada, Ken Sakai, Moriya Ohkuma, Masanori Tohno
A Gram-stain-variable, strictly anaerobic, rod-shaped, catalase-negative and endospore-forming bacterial strain, designated MJC39(T), was isolated from grass silage preserved in Hokkaido, Japan. Growth occurred at 20-42 °C, pH 5.0-7.0 and NaCl concentrations up to 2 % (w/v). The isolated strain MJC39(T) produced butyric acid in peptone yeast extract medium with glucose. The DNA G+C content of strain MJC39(T) was 34.4±0.2 mol%. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and summed feature 3 (including C16 : 1ω7c/C16 : 1ω6c)...
October 16, 2017: International Journal of Systematic and Evolutionary Microbiology
Simon Deusch, Amélia Camarinha-Silva, Jürgen Conrad, Uwe Beifuss, Markus Rodehutscord, Jana Seifert
The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture...
2017: Frontiers in Microbiology
Lillian Wambua, Bernd Schneider, Allan Okwaro, Joseph Odhiambo Wanga, Olive Imali, Peninah Nduku Wambua, Lavender Agutu, Cassandra Olds, Chris Stephen Jones, Daniel Masiga, Charles Midega, Zeyaur Khan, Joerg Jores, Anne Fischer
Napier grass Stunt Disease (NSD) is a severe disease of Napier grass (Pennisetum purpureum) in Eastern Africa, caused by the leafhopper-transmitted bacterium Candidatus Phytoplasma oryzae. The pathogen severely impairs the growth of Napier grass, the major fodder for dairy cattle in Eastern Africa. NSD is associated with biomass losses of up to 70% of infected plants. Diagnosis of NSD is done by nested PCR targeting the phytoplasma DNA, which is difficult to perform in developing countries with little infrastructure...
October 2017: Molecular and Cellular Probes
Rohini Keshava, Nagesh Muniyappa, Rajalakshmi Gope, Ananthanarayana Saligrama Ramaswamaiah
Imperata cylindrica, a tall tufted grass which has multiple pharmacological applications is one of the key ingredients in various traditional medicinal formula used in India. Previous reports have shown that I. cylindrica plant extract inhibited cell proliferation and induced apoptosis in various cancer cell lines. To our knowledge, no studies have been published on the effect of I. cylindrica leaf extract on human oral cancers. The present study was undertaken in order to evaluate the anticancer properties of the leaf extract of I...
2016: Asian Pacific Journal of Cancer Prevention: APJCP
Si Hong Park, Sang In Lee, Steven C Ricke
Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens...
2016: PloS One
Ilma Tapio, Kevin J Shingfield, Nest McKain, Aurélie Bonin, Daniel Fischer, Ali R Bayat, Johanna Vilkki, Pierre Taberlet, Timothy J Snelling, R John Wallace
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons...
2016: PloS One
Pei-Fa Yu, Qing-Li Niu, Zhi-Jie Liu, Ji-Fei Yang, Ze Chen, Gui-Quan Guan, Guang-Yuan Liu, Jian-Xun Luo, Hong Yin
An investigation was performed to detect eight pathogens in ticks collected from grass tips or animals in the southern, central and northeast regions of China. DNA samples extracted from ticks were collected from ten different locations in eight provinces of China and subjected to screening for tick-borne pathogens, including Borrelia burgdorferi sensu lato, Ehrlichia spp., Rickettsia spp., Babesia/Theileria spp., Ehrlichia ruminantium, Coxiella burnetii, and Francisella tularensis, using nested PCR assays and sequencing analysis...
June 2016: Acta Tropica
Melanie B Lengowski, Karin H R Zuber, Maren Witzig, Jens Möhring, Jeannette Boguhn, Markus Rodehutscord
This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum...
2016: PloS One
Amanda Dargay, Reena Roy
Body fluids detected on commonly found crime scene substrates require extraction, purification and quantitation of DNA prior to amplification and generation of short tandem repeat (STR) DNA profiles. In this research Y-STR profiles were generated via direct amplification of blood and saliva deposited on 12 different substrates. These included cigarette butts, straws, grass, leaves, woodchips and seven different types of fabric. After depositing either 0.1 μL of blood or 0.5 μL of saliva, each substrate containing the dry body fluid stain was punched using a Harris 1...
April 2016: Journal of Forensic and Legal Medicine
F Wemheuer, B Wemheuer, D Kretzschmar, B Pfeiffer, S Herzog, R Daniel, S Vidal
UNLABELLED: Most plant species are colonized by endophytic bacteria. Despite their importance for plant health and growth, the response of these bacteria to grassland management regimes is still not understood. Hence, we investigated the bacterial community structure in three agricultural important grass species Dactylis glomerata L., Festuca rubra L. and Lolium perenne L. with regard to fertilizer application and different mowing frequencies. For this purpose, above-ground plant material was collected from the Grassland Management Experiment (GrassMan) in Germany in September 2010 and 2011...
April 2016: Letters in Applied Microbiology
Anthony J Rietl, Megan E Overlander, Andrew J Nyman, Colin R Jackson
Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors such as salinity that control plant zonation in saltmarshes are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA...
February 2016: Microbial Ecology
Matthew Sean McCabe, Paul Cormican, Kate Keogh, Aaron O'Connor, Eoin O'Hara, Rafael Alejandro Palladino, David Anthony Kenny, Sinéad Mary Waters
Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004)...
2015: PloS One
K G Savchenko, L M Carris, L A Castlebury, V P Heluta, S P Wasser, E Nevo
Stripe smut of grasses, Ustilago striiformis s.l., is a complex of smut fungi widely distributed over temperate and subtropical regions. The disease results in the shredding and death of leaf tissue following the rupture of elongated sori. Nearly 100 different grass species in more than 30 genera are infected by stripe smut. During the last two centuries more than 30 smut taxa have been described from members of this complex. The present study attempts to clarify the taxonomy and phylogeny of stripe smuts on grasses by analysing both morphological and molecular data...
December 2014: Persoonia
Madeleine S Bloch, Daniela Paunescu, Philipp R Stoessel, Carlos A Mora, Wendelin J Stark, Robert N Grass
The capability of tracing a food product along its production chain is important to ensure food safety and product authenticity. For this purpose and as an application example, recently developed Silica Particles with Encapsulated DNA (SPED) were added to milk at concentrations ranging from 0.1 to 100 ppb (μg per kg milk). Thereby the milk, as well as the milk-derived products yoghurt and cheese, could be uniquely labeled with a DNA tag. Procedures for the extraction of the DNA tags from the food matrixes were elaborated and allowed identification and quantification of previously marked products by quantitative polymerase chain reaction (qPCR) with detection limits below 1 ppb of added particles...
October 29, 2014: Journal of Agricultural and Food Chemistry
Ken Kraaijeveld, Letty A de Weger, Marina Ventayol García, Henk Buermans, Jeroen Frank, Pieter S Hiemstra, Johan T den Dunnen
Pollen monitoring is an important and widely used tool in allergy research and creation of awareness in pollen-allergic patients. Current pollen monitoring methods are microscope-based, labour intensive and cannot identify pollen to the genus level in some relevant allergenic plant groups. Therefore, a more efficient, cost-effective and sensitive method is needed. Here, we present a method for identification and quantification of airborne pollen using DNA sequencing. Pollen is collected from ambient air using standard techniques...
January 2015: Molecular Ecology Resources
Chhavi Mahajan, B S Chadha, Lata Nain, Amarjeet Kaur
The aim of this work was to evaluate glycosyl hydrolases produced by diverse thermophilic fungal strains for saccharification of alkali and biologically (Trametes hirusita/Myrothecium roridum) treated Parthenium hysterophorus and rice straw. The compositional analysis of hydrolysates by HPLC showed distinct profiles of hexose, pentose and oligomeric sugars. Malbranchea cinnamomea was most efficient source of glycosyl hydrolases producing 283.8, 35.9, 129.6, 27,193, 4.66, 7.26(units/gds) of endoglucanase, cellobiohydrolase, β-glucosidase, xylanase, α-αrabinofuranosidase and β xylosidase, respectively...
July 2014: Bioresource Technology
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