Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.

Background: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome.

Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels.

Arginine, glutamic acid and selenocysteine based codon bias has been shown to regulate the translation of specific mRNAs for proteins that participate in stress responses, cell cycle and transcriptional regulation. Defining codon-bias in gene networks has the potential to identify other pathways under translational control. Here we have used computational methods to analyze the ORFeome of all unique human (19,711) and mouse (22,138) open-reading frames (ORFs) to characterize codon-usage and codon-bias in genes and biological processes.

Rational selection of morphological phenotypic traits to extract essential similarities in chemical perturbation in the ergosterol pathway.

Terbinafine, fluconazole, and amorolfine inhibit fungal ergosterol synthesis by acting on their target enzymes at different steps in the synthetic pathway, causing the accumulation of various intermediates. We found that the effects of these three in- hibitors on yeast morphology were different. The number of morphological parameters commonly altered by these drugs was only approximately 6% of the total.

Systematic data analysis pipeline for quantitative morphological cell phenotyping.

Quantitative morphological phenotyping (QMP) is an image-based method used to capture morphological features at both the cellular and population level. Its interdisciplinary nature, spanning from data collection to result analysis and interpretation, can lead to uncertainties, particularly among those new to this actively growing field. High analytical specificity for a typical QMP is achieved through sophisticated approaches that can leverage subtle cellular morphological changes.

Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.

Background: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically-reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by and gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome.

Application of unimodal probability distribution models for morphological phenotyping of budding yeast.

Morphological phenotyping of the budding yeast Saccharomyces cerevisiae has helped to greatly clarify the functions of genes and increase our understanding of cellular functional networks. It is necessary to understand cell morphology and perform quantitative morphological analysis (QMA) but assigning precise values to morphological phenotypes has been challenging. We recently developed the Unimodal Morphological Data image analysis pipeline for this purpose.

Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans.

DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to begin to define the landscape of DNA modifications in rat and human tissues. A basis set of 114 putative DNA adducts was identified in heart, liver, brain, and kidney in 1-26-month-old rats and 111 in human heart and brain by 'stepped MRM' LC-MS/MS.

Targeted Mutations Produce Divergent Characteristics in Pedigreed Sake Yeast Strains.

Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same target mutation is introduced into different genetic backgrounds is unclear. In a previous study, we performed genome editing of , , , and on the standard sake yeast strain Kyokai No.

Assignment of unimodal probability distribution models for quantitative morphological phenotyping.

Background: Cell morphology is a complex and integrative readout, and therefore, an attractive measurement for assessing the effects of genetic and chemical perturbations to cells. Microscopic images provide rich information on cell morphology; therefore, subjective morphological features are frequently extracted from digital images. However, measured datasets are fundamentally noisy; thus, estimation of the true values is an ultimate goal in quantitative morphological phenotyping.

Are droplets really suitable for single-cell analysis? A case study on yeast in droplets.

Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases.

Defining Functions of Mannoproteins in by High-Dimensional Morphological Phenotyping.

Mannoproteins are non-filamentous glycoproteins localized to the outermost layer of the yeast cell wall. The physiological roles of these structural components have not been completely elucidated due to the limited availability of appropriate tools. As the perturbation of mannoproteins may affect cell morphology, we investigated mannoprotein mutants in via high-dimensional morphological phenotyping.

Genome Editing to Generate Sake Yeast Strains with Eight Mutations That Confer Excellent Brewing Characteristics.

Sake yeast is mostly diploid, so the introduction of recessive mutations to improve brewing characteristics requires considerable effort. To construct sake yeast with multiple excellent brewing characteristics, we used an evidence-based approach that exploits genome editing technology. Our breeding targeted the , , , and genes.

Genome editing to generate nonfoam-forming sake yeast strains.

Mutations frequently occur during breeding of sake yeasts and result in unexpected phenotypes. Here, genome editing tools were applied to develop an ideal nonfoam-forming sake yeast strain, K7GE01, which had homozygous / deletion alleles that were responsible for nonfoam formation and few off-target mutations. High-dimensional morphological phenotyping revealed no detectable morphological differences between the genome-edited strain and its parent, while the canonical nonfoam-forming strain, K701, showed obvious morphological changes.

A Novel LSSVM Based Algorithm to Increase Accuracy of Bacterial Growth Modeling.

Background: The recent progress and achievements in the advanced, accurate, and rigorously evaluated algorithms has revolutionized different aspects of the predictive microbiology including bacterial growth.

Objectives: In this study, attempts were made to develop a more accurate hybrid algorithm for predicting the bacterial growth curve which can also be applicable in predictive microbiology studies.

Materials And Methods: Sigmoid functions, including Logistic and Gompertz, as well as least square support vector machine (LSSVM) based algorithms were employed to model the bacterial growth of the two important strains comprising and .

Genetic dissection of the signaling pathway required for the cell wall integrity checkpoint.

The cell wall integrity checkpoint monitors synthesis of cell wall materials during the cell cycle. Upon perturbation of cell wall synthesis, the cell wall integrity checkpoint is activated, downregulating Clb2 transcription. Here, we identified genes involved in this checkpoint by genetic screening of deletion mutants.

Systematic analysis of Ca homeostasis in based on chemical-genetic interaction profiles.

We investigated the global landscape of Ca homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca-sensitive () mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca- interactions. We found that high-dimensional, morphological Ca- interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca- interactions were all negative in principle.

Plant dehydrins: shedding light on structure and expression patterns of dehydrin gene family in barley.

Dehydrins, an important group of late embryogenesis abundant proteins, accumulate in response to dehydration stresses and play protective roles under stress conditions. Herein, phylogenetic analysis of the dehydrin family was performed using the protein sequences of 108 dehydrins obtained from 14 plant species based on plant taxonomy and protein subclasses. Sub-cellular localization and phosphorylation sites of these proteins were also predicted.