Improved Representation of Biological Information by Using Correlation as Distance Function for Heatmap Cluster Analysis

Tiessen, Axel; Cubedo-Ruiz, Edgar A.; Winkler, Robert

doi:10.4236/ajps.2017.83035

Cited by 18 publications

(12 citation statements)

References 29 publications

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“…Several heatmap-bicluster figures were constructed, selecting the significant negative ions only ( S2 Fig ), all the significant positive ions ( Fig 1D ), or only the most intense significant positive ions ( S3 Fig ). In all cases, an optimized hierarchical clustering based on correlation as previously described was applied [ 49 ]. Those grayscale heatmaps depicted the relative intensity (ion abundance) under the different conditions (black indicates high, and white indicates low, as shown in Fig 1D and S2 and S3 Figs).…”

Section: Resultsmentioning

confidence: 99%

High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response

et al. 2020

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Sugars act not only as substrates for plant metabolism, but also have a pivotal role in signaling pathways. Glucose signaling has been widely studied in the vascular plant Arabidopsis thaliana, but it has remained unexplored in non-vascular species such as Physcomitrella patens. To investigate P. patens response to high glucose treatment, we explored the dynamic changes in metabolism and protein population by applying a metabolomic fingerprint analysis (DIESI-MS), carbohydrate and chlorophyll quantification, Fv/Fm determination and label-free untargeted proteomics. Glucose feeding causes specific changes in P. patens metabolomic fingerprint, carbohydrate contents and protein accumulation, which is clearly different from those of osmotically induced responses. The maximal rate of PSII was not affected although chlorophyll decreased in both treatments. The biological process, cellular component, and molecular function gene ontology (GO) classifications of the differentially expressed proteins indicate the translation process is the most represented category in response to glucose, followed by photosynthesis, cellular response to oxidative stress and protein refolding. Importantly, although several proteins have high fold changes, these proteins have no predicted identity. The most significant discovery of our study at the proteome level is that high glucose increase abundance of proteins related to the translation process, which was not previously evidenced in non-vascular plants, indicating that regulation by glucose at the translational level is a partially conserved response in both plant lineages. To our knowledge, this is the first time that metabolome fingerprint and proteomic analyses are performed after a high sugar treatment in non-vascular plants. These findings unravel evolutionarily shared and differential responses between vascular and non-vascular plants.

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Section: Resultsmentioning

confidence: 99%

High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response

et al. 2020

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“…Data transformation using 'normalize' was used to compare and group different data. In addition, heatmap cluster Figures 1 and 2 were used to summarize the data from the experiment according to Euclidean distance [94]. The relationship between the parameters was determined with the Pearson correlation coefficient.…”

Section: Discussionmentioning

confidence: 99%

Growth and Photosynthetic Activity of Selected Spelt Varieties (Triticum aestivum ssp. spelta L.) Cultivated under Drought Conditions with Different Endophytic Core Microbiomes

Ratajczak

Sulewska

Błaszczyk

et al. 2020

IJMS

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The role of the microbiome in the root zone is critically important for plants. However, the mechanism by which plants can adapt to environmental constraints, especially water deficit, has not been fully investigated to date, while the endophytic core microbiome of the roots of spelt (Triticum aestivum ssp. spelta L.) grown under drought conditions has received little attention. In this study, we hypothesize that differences in the endophytic core of spelt and common wheat root microbiomes can explain the variations in the growth and photosynthetic activity of those plants, especially under drought conditions. Our greenhouse experimental design was completely randomized in a 2 × 4 × 3 factorial scheme: two water regime levels (well-watered and drought), three spelt varieties (T. aestivum ssp. spelta L.: ‘Badenstern’, ‘Badenkrone’ and ‘Zollernspelz’ and one wheat variety: T. aestivum ssp. vulgare L: ‘Dakotana’) and three mycorrhizal levels (autoclaved soil inoculation with Rhizophagus irregularis, control (autoclaved soil) and natural inoculation (non-autoclaved soil—microorganisms from the field). During the imposed stress period, relative water content (RWC), leaf chlorophyll fluorescence, gas exchange and water use efficiency (WUE) were measured. Microscopic observations of the root surface through fungi isolation and identification were conducted. Our results indicate that ‘Badenstern’ was the most drought tolerant variety, followed by ‘Zollernspelz’ and ‘Badenkrone,’ while the common wheat variety ‘Dakotana’ was the most drought sensitive. Inoculation of ‘Badenstern’ with the mycorrhizal fungi R. irregularis contributed to better growth performance as evidenced by increased whole plant and stalk dry matter accumulation, as well as greater root length and volume. Inoculation of ‘Zollernspelz’ with arbuscular mycorrhizal fungi (AMF) enhanced the photochemical efficiency of Photosystem II and significantly improved root growth under drought conditions, which was confirmed by enhanced aboveground biomass, root dry weight and length. This study provides evidence that AMF have the potential to be beneficial for plant growth and dry matter accumulation in spelt varieties grown under drought conditions.

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“…We then grouped bacterial taxa into clusters based on similarities in age-associated abundance trajectories. Pairwise distances between microbial taxa trajectories (i.e., the predicted values of the LOESS regression) were computed using correlation coefficients as a distance measure [150], and hierarchical clustering was performed using the complete method (using the function hclust from the stats R package). The optimal number of clusters was determined using the Elbow method (i.e., choosing a number of clusters so that adding another cluster does not highly improve the total within-cluster sum of squares) [151].…”

Section: Age-associated Changes In Microbial Taxonomic Compositionmentioning

confidence: 99%

Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

Baniel

Petrullo

Mercer

et al. 2021

Preprint

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Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mother’s milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more “milk-oriented” compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization in early life and the role of maternal effects in modulating this trajectory in a wild primate.

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Improved Representation of Biological Information by Using Correlation as Distance Function for Heatmap Cluster Analysis

Cited by 18 publications

References 29 publications

High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response

High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response

Growth and Photosynthetic Activity of Selected Spelt Varieties (Triticum aestivum ssp. spelta L.) Cultivated under Drought Conditions with Different Endophytic Core Microbiomes

Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

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