The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean models, with the aim determining feasible rule structures, given requirement stable solutions generated networks. We find that, for ensembles those canalyzing rules are remarkably stable, whereas random only marginally stable. Furthermore, substantial parts networks frozen, sense that they reach same state, regardless initial state. Thus, our ensemble approach suggests shows highly ordered dynamics.

Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to fungi in exchange for nitrogen, and this process is critical nitrogen carbon cycles forest ecosystems. However, extents which can liberate modify soil organic matter mechanisms by they do so remain unclear since have lost many enzymes litter decomposition that were present their free-living, saprotrophic ancestors. Using time-series spectroscopy transcriptomics, we examined ability of two...

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety architectures. For all power law, exponential, flat in-degree distributions, we find that the networks are dynamically stable. Furthermore, architectures few inputs per node, dynamics is close to critical. In addition, fraction genes active decreases number node. These results based upon investigating ensembles using analytical methods. Also, different numbers fixed...

Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture transcriptional regulatory circuitry responsible for cell determination, which involves transcription factors OCT4, SOX2, NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target involved in maintenance differentiation cells. A search OCT4–SOX2–NANOG network motif species reveals that it is unique mammals. With a kinetic modeling approach, we...

The Kauffman model describes a particularly simple class of random Boolean networks. Despite the simplicity model, it exhibits complex behavior and has been suggested as for real world network problems. We introduce novel approach to analyzing attractors in networks, applying networks we prove that average number grows faster than any power law with system size.

Abstract The majority of nitrogen in forest soils is found organic matter–protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role decomposing and mobilizing from such However, little known about the mechanisms governing these processes, how they regulated by carbon host plant availability more easily available forms sources. Here we used spectroscopic analyses transcriptome profiling examine presence or absence glucose and/or ammonium regulates decomposition litter...

Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes light and other environmental factors. The complexity the circadian clock higher plants makes it difficult understand role individual genes or molecular interactions, mathematical modelling has been useful guiding research model organisms such as Arabidopsis thaliana. We present a Arabidopsis, based on large corpus published course data. It appears from...

Summary Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth‐limiting nutrients, such as nitrogen (N), which mainly occurs proteins complexed in soil organic matter ( SOM ). The mechanisms for liberating this N are unclear fungi have lost many genes encoding lignocellulose‐degrading enzymes present saprotrophic ancestors. We hypothesized that hydroxyl radicals ˙ OH ), produced by the fungus Paxillus involutus during growth , involved N. was grown 7 d N‐containing or...

Circadian clocks were, until recently, seen as a consequence of rhythmic transcription clock components, directed by transcriptional/translational feedback loops (TTFLs). Oscillations protein modification were then discovered in cyanobacteria. Canonical posttranslational signaling processes have known importance for across taxa. More evidence from the unicellular eukaryote Ostreococcus tauri revealed transcription-independent, shared anucleate human cells. In this study, system reveals...

Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable environmental changes. Detailed understanding the circadian network higher plants, such as Arabidopsis thaliana, is hampered by high number partially redundant genes. However, picoeukaryotic alga Ostreococcus tauri, which was recently shown possess a small non-redundant clock genes, presents an attractive alternative target for detailed modelling green lineage. Based on...

Abstract Filamentous fungi play a key role as decomposers in Earth’s nutrient cycles. In soils, substrates are heterogeneously distributed microenvironments. Hence, individual hyphae of mycelium may experience very different environmental conditions simultaneously. the current work, we investigated how cope with local variations at single-cell level. We developed method based on infrared spectroscopy that allows direct, in-situ chemical imaging decomposition activity hyphal tips. Colonies...

ABSTRACT In microbiological studies, a common goal is to link environmental factors microbial activities. Both and activities are typically derived from bulk samples. It becoming increasingly clear that such parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, spatial distribution of chemical compound classes can be visualized, making it useful tool for studying interactions between cells their microenvironments. The...

Abstract Background Signal transduction pathways convey information from the outside of cell to transcription factors, which in turn regulate gene expression. Our objective is analyze tumor expression data microarrays context such pathways. Results We use compiled TRANSPATH/TRANSFAC databases and literature, three publicly available cancer microarray sets. Variation pathway activity, across samples, gauged by degree correlation between downstream targets a pathway. Two scores are applied;...

Recent experiments uncovered a mutational pathway between two proteins, along which single mutation causes switch in fold. Searching for such paths real proteins remains, despite this achievement, true challenge. Here, we analyze fold switching the minimalistic hydrophobic/polar model on square lattice. For analysis, generate comprehensive sequence-structure database chains of length ⩽ 30, exceeds previous work by five units. Single-mutation-induced turns out to be quite common model. The...

Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of green alga Ostreococcus tauri is simplest plant discovered so far. Its many advantages as an experimental system facilitate testing computational predictions. We present a model in stochastic process algebra Bio-PEPA and exploit its mapping different analysis techniques, such ordinary differential equations, simulation algorithms model-checking. small number molecules...

Summary The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes to the most appropriate of day. interlocking feedback loop mechanism is conserved species; however, number loops varies. Mathematical and computational analyses have suggested that complexity affects overall flexibility oscillator, including its responses entrainment signals. We used discriminating experimental assay, at transition between different photoperiods, in order test...

Modern vibrational spectroscopy techniques enable the rapid collection of thousands spectra in a single hyperspectral image, allowing researchers to study spatially heterogeneous samples at micrometer resolution. A number algorithms have been developed correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. After preprocessing, are commonly decomposed clustered reveal informative patterns subtle spectral changes. Several these...

In the dawning era of artificial intelligence (AI), health care stands to undergo a significant transformation with increasing digitalization patient data. Digital imaging, in particular, will serve as an important platform for AI aid decision making and diagnostics. A growing number studies demonstrate potential automatic pre-surgical skin tumor delineation, which could have tremendous impact on clinical practice. However, current methods rely having ground truth images borders are already...

Background Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which virtually universal microorganisms. The lac operon E. coli but one example how enzyme and transporter production can be made conditional on presence nutrient to catabolize. Methodology With minimalist model metabolism, cell growth transcriptional microorganism, we explore interaction between environmental conditions gene set rate cells phase exponential growth. This silico model,...