The Local Edge Machine: inference of dynamic models of gene regulation

We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle. Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks.Department of Applied Mathematic

The Third International Symposium on Fungal Stress – ISFUS

Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International Symposium on Fungal Stress (ISFUS) brings together leading scientists from around the world who research fungal stress. This article discusses presentations given at the third ISFUS, held in São José dos Campos, São Paulo, Brazil in 2019, thereby summarizing the state-of-the-art knowledge on fungal stress, a field that includes microbiology, agriculture, environmental science, ecology, biotechnology, medicine, and astrobiology

Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability.

Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, <i>Cryptococcus neoformans</i>

<div><p>The pathogenic yeast <i>Cryptococcus neoformans</i> causes fungal meningitis in immune-compromised patients. Cell proliferation in the budding yeast form is required for <i>C</i>. <i>neoformans</i> to infect human hosts, and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation. Thus, understanding cell-cycle regulation is critical for a full understanding of virulence factors for disease. Our group and others have demonstrated that a large fraction of genes in <i>Saccharomyces cerevisiae</i> is expressed periodically during the cell cycle, and that proper regulation of this transcriptional program is important for proper cell division. Despite the evolutionary divergence of the two budding yeasts, we found that a similar percentage of all genes (~20%) is periodically expressed during the cell cycle in both yeasts. However, the temporal ordering of periodic expression has diverged for some orthologous cell-cycle genes, especially those related to bud emergence and bud growth. Genes regulating DNA replication and mitosis exhibited a conserved ordering in both yeasts, suggesting that essential cell-cycle processes are conserved in periodicity and in timing of expression (i.e. duplication before division). In <i>S</i>. <i>cerevisiae</i> cells, we have proposed that an interconnected network of periodic transcription factors (TFs) controls the bulk of the cell-cycle transcriptional program. We found that temporal ordering of orthologous network TFs was not always maintained; however, the TF network topology at cell-cycle commitment appears to be conserved in <i>C</i>. <i>neoformans</i>. During the <i>C</i>. <i>neoformans</i> cell cycle, DNA replication genes, mitosis genes, and 40 genes involved in virulence are periodically expressed. Future work toward understanding the gene regulatory network that controls cell-cycle genes is critical for developing novel antifungals to inhibit pathogen proliferation.</p></div

About 20% of all <i>S</i>. <i>cerevisiae</i> and <i>C</i>. <i>neoformans</i> genes are periodically expressed during the cell cycle.

<p>Four periodicity-ranking algorithms were run on the time series gene expression datasets at a period of 75 minutes (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006453#pgen.1006453.s001" target="_blank">S1 File</a>). The top-ranked periodic genes (1–1600) were then filtered by the Lomb-Scargle algorithm to identify (<b>A</b>) 1246 periodic genes in <i>S</i>. <i>cerevisiae</i> and (<b>B</b>) 1134 periodic genes in <i>C</i>. <i>neoformans</i>. Genes in each periodic gene list were ordered along the y-axis by peak time of expression in the respective yeast dataset. As expected, the second and third cell cycles showed expression level damping due to asymmetric cell divisions in both budding yeasts. Transcript levels are depicted as a z-score change relative to mean expression for each gene, where values represent the number of standard deviations away from the mean. Each row represents transcript levels of a unique gene across the time series. Each column represents a time point in minutes.</p

Population synchrony for <i>S</i>. <i>cerevisiae</i> and <i>C</i>. <i>neoformans</i> over > 2 cell cycles.

<p><i>S</i>. <i>cerevisiae</i> cells were grown in 2% YEPD media, synchronized by alpha-factor mating pheromone, and released into YEPD (<b>A</b>) <i>C</i>. <i>neoformans</i> cells were grown in 2% YEPD rich media; small daughter cells were isolated by centrifugal elutriation and released into YEPD (<b>B</b>). Population synchrony was estimated by counting at least 200 cells per time point for the presence or absence of a bud, and doubling time was also monitored (<b>C-D</b>). Orange arrows indicate the time points where each population passed a complete doubling in cell concentration from the previous cycle (gray lines).</p