Use of Bayesian Statistics for Pairwise Comparison of Megavariate Data Sets: Extracting Meaningful Differences between GCxGC-MS Chromatograms Using Jensen–Shannon Divergence

Barcaru, Andrei; Vivó-Truyols, Gabriel

doi:10.1021/acs.analchem.5b03506

Cited by 14 publications

(16 citation statements)

References 20 publications

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“…In addition to the measurement of TAG content and DU, SCRS can serve as a comprehensive ‘biochemical fingerprint’ of a cell (Butler et al ., 2016; He et al ., 2019; Huang et al ., 2004; Lorenz et al ., 2017). Jensen−Shannon distances (JSDs), which measure difference of frequency spectra (Barcaru and Vivo‐Truyols, 2016; Iwasaki et al ., 2017), can be used to measure the SCRS‐based phenotypic difference between two cells. As for the phenotype difference among strains, we proposed ‘strain‐ramanome’ to define the series of ramanomes for a certain strain at a set of time points or inducing conditions.…”

Section: Resultsmentioning

confidence: 99%

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Wang

Gong

et al. 2021

The Plant Journal

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Industrial microalgae are promising photosynthetic cell factories, yet tools for large-scale targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we established a method to precisely and serially delete large genome fragments of~100 kb from its 30.01 Mb nuclear genome. We started by identifying the 'non-essential' chromosomal regions (i.e. low expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is~98 kb in size, located near the telomere of the 502.09-kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing the distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also achieved double-deletion of both LER1 and LER2 (from Chr 9) that total~214 kb at maximum, which can result in slightly higher growth rate and biomass productivity than the wild-type. Therefore, loss of the large, yet 'non-essential' regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions had not been previously reported in microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.

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Section: Resultsmentioning

confidence: 99%

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Wang

Gong

et al. 2021

The Plant Journal

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“…It is the opinion of the authors that the proposed method can be successfully applied in different fields. The only requirement is a reasonable resolution [102].…”

Section: Data Handlingmentioning

confidence: 99%

Advanced mono‐ and multi‐dimensional gas chromatography–mass spectrometry techniques for oxygen‐containing compound characterization in biomass and biofuel samples

Beccaria

Siqueira

Maniquet

et al. 2020

J of Separation Science

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A wide variety of biomass, from triglycerides to lignocellulosic‐based feedstock, are among promising candidates to possibly fulfill requirements as a substitute for crude oils as primary sources of chemical energy feedstock. During the feedstock processing carried out to increase the H:C ratio of the products, heteroatom‐containing compounds can promote corrosion, thus limiting and/or deactivating catalytic processes needed to transform the biomass into fuel. The use of advanced gas chromatography techniques, in particular multi‐dimensional gas chromatography, both heart‐cutting and comprehensive coupled to mass spectrometry, has been widely exploited in the field of petroleomics over the past 30 years and has also been successfully applied to the characterization of volatile and semi‐volatile compounds during the processing of biomass feedstock. This review intends to describe advanced gas chromatography–mass spectrometry‐based techniques, mainly focusing in the period 2011–early 2020. Particular emphasis has been devoted to the multi‐dimensional gas chromatography–mass spectrometry techniques, for the isolation and characterization of the oxygen‐containing compounds in biomass feedstock. Within this context, the most recent advances to sample preparation, derivatization, as well as gas chromatography instrumentation, mass spectrometry ionization, identification, and data handling in the biomass industry, are described.

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“…In addition to the TAG content and DU prediction, SCRS can also estimate the 'fingerprint' of a cell (86)(87)(88). Jensen-Shannon distances (JSD), which usually adapted for measuring the difference of frequency spectra (89,90), could be used to measure the phenotypic difference between pairwise cells based on its SCRS. Moreover, to compare the phenotype difference among strains, here, we proposed 'strain-Ramanome' to define a certain strain, which consists of ramanomes of one certain strain at multiple inducing conditions and timepoints.…”

Section: Phenotypes Of the Ler1 Deletion Mutantsmentioning

confidence: 99%

Genome engineering ofNannochloropsiswith large deletions for constructing microalgal minigenomes

Wang

Gong

et al. 2020

Preprint

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Industrial microalgae are promising photosynthetic cell factories, yet tools for targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica we established a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01-Mb nuclear genome. We started by identifying the “non-essential” chromosomal regions (i.e., low-expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is ~98 kb in size, located near the telomere of the 502.09 kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also performed double-deletion of both LER1 and LER2 (from Chr 9) that totals ~214 kb, and phenotypes are essentially normal. Therefore, loss of the large yet “non-essential” regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions have not been reported in plants or microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.

show abstract

Use of Bayesian Statistics for Pairwise Comparison of Megavariate Data Sets: Extracting Meaningful Differences between GCxGC-MS Chromatograms Using Jensen–Shannon Divergence

Cited by 14 publications

References 20 publications

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Advanced mono‐ and multi‐dimensional gas chromatography–mass spectrometry techniques for oxygen‐containing compound characterization in biomass and biofuel samples

Genome engineering ofNannochloropsiswith large deletions for constructing microalgal minigenomes

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