Untitled

Novák, Jaroslav; Kim, Seon‐Young; Xu, Jun; Modlich, Olga; Volsky, David J.; Honys, David; Slonczewski, Joan L.; Bell, Douglas A.; Blattner, Fred R.; Blumwald, Eduardo; Boerma, Marjan; Cosio, Manuel G.; Gatalica, Zoran; Hajdúch, Marián; Hidalgo, Juan; McInnes, Roderick R.; Miller, Mia; Penkowa, Milena; Rolph, Michael S.; Sottosanto, Jordan B.; St‐Arnaud, René; Szego, Michael J.; Twell, David; Wang, Charles

doi:10.1186/1745-6150-1-27

Cited by 13 publications

(5 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Subsequent BLASTP analysis ( Camacho et al, 2009 ) of predicted proteins indicated that only one circular contig had viral hallmark genes, meanwhile nine contigs had genes associated with bacterial mobile genetic elements and one contig remain completely unknown. These hallmark genes are shared by many viruses but are absents from cellular genomes ( Koonin et al, 2006 ). VirSorter tool analysis ( Roux et al, 2015a ) confirmed these results, obtaining the same complete putative viral contig from the 58°C assembly, 40,740 bp long and 43.9% of GC content.…”

Section: Resultsmentioning

confidence: 99%

Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

et al. 2018

View full text Add to dashboard Cite

Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), taxonomic composition (metagenomics), and active infectivity (metatranscriptomics) of viral communities over a thermal gradient in hot spring phototrophic mats from Northern Patagonia (Chile). The mats were dominated (up to 53%) by cosmopolitan thermophilic filamentous true-branching cyanobacteria from the genus Mastigocladus, the associated viral community was predominantly composed of Caudovirales (70%), with most of the active infections driven by cyanophages (up to 90% of Caudovirales transcripts). Metagenomic assembly lead to the first full genome description of a T7-like Thermophilic Cyanophage recovered from a hot spring (Porcelana Hot Spring, Chile), with a temperature of 58°C (TC-CHP58). This could potentially represent a world-wide thermophilic lineage of podoviruses that infect cyanobacteria. In the hot spring, TC-CHP58 was active over a temperature gradient from 48 to 66°C, showing a high population variability represented by 1979 single nucleotide variants (SNVs). TC-CHP58 was associated to the Mastigocladus spp. by CRISPR spacers. Marked differences in metagenomic CRISPR loci number and spacers diversity, as well as SNVs, in the TC-CHP58 proto-spacers at different temperatures, reinforce the theory of co-evolution between natural virus populations and cyanobacterial hosts. Considering the importance of cyanobacteria in hot spring biogeochemical cycles, the description of this new cyanopodovirus lineage may have global implications for the functioning of these extreme ecosystems.

show abstract

Section: Resultsmentioning

confidence: 99%

Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

et al. 2018

View full text Add to dashboard Cite

show abstract

“…MeDIP was selected among many other methods for methylation profiling because it is one of the few methods that is feasible for studying genome-wide methylation differences between groups of subjects, it has been successfully applied in many published studies (Feber et al; Weber et al, 2005; Keshet et al, 2006; Novak et al, 2006; Zhang, 2006; Cheng et al, 2008; Down et al, 2008; Tomazou et al, 2008; Liu et al, 2009; Murphy et al, 2009; Takeshima et al, 2009; Bell et al, 2010; Cheung et al, 2010; Flanagan et al, 2010; Guerrero-Bosagna et al, 2010; Gunther and Grundhoff, 2010; Hiura et al, 2010; Movassagh et al, 2010; Tsui et al, 2010; Lempiainen et al, 2011; Morris et al, 2011), and it has been found competitive with the other high-throughput profiling methods that are in use (Irizarry et al, 2008; Jia et al, 2010; Jin et al, 2010; Robinson et al, 2010; Nair et al, 2011; Rajendram et al, 2011; Yang et al, 2011). Moreover, MeDIP detects DNA methylation exclusively from hydroxymethylation and is not confounded by chemical conversion and biased amplification of converted sequences.…”

Section: Methodsmentioning

confidence: 99%

The Signature of Maternal Rearing in the Methylome in Rhesus Macaque Prefrontal Cortex and T Cells

et al. 2012

View full text Add to dashboard Cite

Early life adversity is associated with a broad scope of life-long health and behavioral disorders. Particularly critical is the role of the mother. A possible mechanism is that these effects are mediated by “epigenetic” mechanisms. Studies in rodents suggest a causal relationship between early life adversity and changes in DNA methylation in several “candidate genes” in the brain. This study examines whether randomized differential rearing (maternal versus surrogate-peer rearing) of rhesus macaques is associated with differential methylation in early adulthood. The data presented here shows that differential rearing leads to differential DNA methylation in both prefrontal cortex and T cells. These differentially methylated promoters tend to cluster both by chromosomal region as well as by gene function. The broad impact of maternal rearing on DNA methylation in both the brain and T cells supports the hypothesis that the response to early-life adversity is system-wide and genome-wide and persists to adulthood. Our data also points to the feasibility of studying the impact of the social environment in peripheral T cells DNA methylation.

show abstract

“…For most datasets, a t -distribution with degrees of freedom between 3 and 5 got the highest posterior probability. This indicates the need of robust noise models, which can handle outlying data points well and suggests that Gaussian noise models are unsuitable for microarray data analysis, even if according to Novak et al (2006 ) only about 5–15% of samples are non-Gaussian distributed.…”

Section: Resultsmentioning

confidence: 99%

“…Similar methods let Hardin and Wilson (2009 ) conclude that microarray data require heavy-tailed noise models. The conclusion of Novak et al (2006 ) was that 5–15% of genes are non-Gaussian distributed, with the majority following Gaussian distributions. Finding such diverse conclusions about noise in microarray data suggest an in-depth investigation of this issue.…”

Section: Introductionmentioning

confidence: 99%

Biological assessment of robust noise models in microarray data analysis

2011

View full text Add to dashboard Cite

Motivation: Although several recently proposed analysis packages for microarray data can cope with heavy-tailed noise, many applications rely on Gaussian assumptions. Gaussian noise models foster computational efficiency. This comes, however, at the expense of increased sensitivity to outlying observations. Assessing potential insufficiencies of Gaussian noise in microarray data analysis is thus important and of general interest.Results: We propose to this end assessing different noise models on a large number of microarray experiments. The goodness of fit of noise models is quantified by a hierarchical Bayesian analysis of variance model, which predicts normalized expression values as a mixture of a Gaussian density and t-distributions with adjustable degrees of freedom. Inference of differentially expressed genes is taken into consideration at a second mixing level. For attaining far reaching validity, our investigations cover a wide range of analysis platforms and experimental settings. As the most striking result, we find irrespective of the chosen preprocessing and normalization method in all experiments that a heavy-tailed noise model is a better fit than a simple Gaussian. Further investigations revealed that an appropriate choice of noise model has a considerable influence on biological interpretations drawn at the level of inferred genes and gene ontology terms. We conclude from our investigation that neglecting the over dispersed noise in microarray data can mislead scientific discovery and suggest that the convenience of Gaussian-based modelling should be replaced by non-parametric approaches or other methods that account for heavy-tailed noise.Contact: peter.sykacek@boku.ac.atAvailability: http://bioinf.boku.ac.at/alexp/robmca.html.

show abstract

Untitled

Cited by 13 publications

References 52 publications

Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

The Signature of Maternal Rearing in the Methylome in Rhesus Macaque Prefrontal Cortex and T Cells

Biological assessment of robust noise models in microarray data analysis

Contact Info

Product

Resources

About