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Limited By:	Subject = Ribosomal RNA;

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Displaying Results 1 - 4 of 4 on page 1 of 1

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Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions (2020)

Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions (2020)

Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.

Abstract:

The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were simi...

http://hdl.handle.net/11019/2300

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Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis (2016)

Clooney, Adam G.; Fouhy, Fiona; Sleator, Roy D.; O'Driscoll, Aisling; Stanton, Cat...

Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis (2016)

Clooney, Adam G.; Fouhy, Fiona; Sleator, Roy D.; O'Driscoll, Aisling; Stanton, Catherine; Cotter, Paul D.; Claesson, Marcus J.

Abstract:

Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest vari...

http://hdl.handle.net/10468/3654

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Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use (2016)

Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.

Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use (2016)

Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.

Abstract:

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transc...

http://hdl.handle.net/10468/3187

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The Effect of Feeding Bt MON810 Maize to Pigs for 110 Days on Intestinal Microbiota (2015)

Buzoianu, Stefan G.; Walsh, Maria C.; Rea, Mary; O'Sullivan, Orla; Crispie, Fiona;...

The Effect of Feeding Bt MON810 Maize to Pigs for 110 Days on Intestinal Microbiota (2015)

Buzoianu, Stefan G.; Walsh, Maria C.; Rea, Mary; O'Sullivan, Orla; Crispie, Fiona; Cotter, Paul D.; Ross, R Paul; Gardiner, Gillian E.; Lawlor, Peadar G

Abstract:

Objective To assess the effects of feeding Bt MON810 maize to pigs for 110 days on the intestinal microbiota. Methodology/Principal Findings Forty male pigs (~40 days old) were blocked by weight and litter ancestry and assigned to one of four treatments; 1) Isogenic maize-based diet for 110 days (Isogenic); 2) Bt maize-based diet (MON810) for 110 days (Bt); 3) Isogenic maize-based diet for 30 days followed by a Bt maize-based diet for 80 days (Isogenic/Bt); 4) Bt maize-based diet for 30 days followed by an isogenic maize-based diet for 80 days (Bt/Isogenic). Enterobacteriaceae, Lactobacillus and total anaerobes were enumerated in the feces using culture-based methods on days 0, 30, 60 and 100 of the study and in ileal and cecal digesta on day 110. No differences were found between treatments for any of these counts at any time point. The relative abundance of cecal bacteria was also determined using high-throughput 16 S rRNA gene sequencing. No differences were observed in any ba...

http://hdl.handle.net/11019/807

Displaying Results 1 - 4 of 4 on page 1 of 1