Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants.

Background: Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive.

Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network.

Motivation: Clustering spatial-resolved gene expression is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression co-localizations in tissue for detecting spatial expression patterns or functional relationships among the genes for biological interpretation in the spatial context. In this article, we present a convolutional neural network (CNN) regularized by the graph of protein-protein interaction (PPI) network to cluster spatially resolved gene expression.

Abiotic stress through time.

Throughout plant evolution the circadian clock has expanded into a complex signaling network, coordinating physiological and metabolic processes with the environment. Early land plants faced new environmental pressures that required energy-demanding stress responses. Integrating abiotic stress response into the circadian system provides control over daily energy expenditure.

Altered Domain Structure of the Prion Protein Caused by Cu Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR.

The cellular isoform of the prion protein (PrP) serves as precursor to the infectious isoform (PrP), and as a cell-surface receptor, which binds misfolded protein oligomers as well as physiological ligands such as Cu ions. PrP consists of two domains: a flexible N-terminal domain and a structured C-terminal domain. Both the physiological and pathological functions of PrP depend on intramolecular interactions between these two domains, but the specific amino acid residues involved have proven challenging to define.

The N-terminus of the prion protein is a toxic effector regulated by the C-terminus.

PrP, the cellular isoform of the prion protein, serves to transduce the neurotoxic effects of PrP, the infectious isoform, but how this occurs is mysterious. Here, using a combination of electrophysiological, cellular, and biophysical techniques, we show that the flexible, N-terminal domain of PrP functions as a powerful toxicity-transducing effector whose activity is tightly regulated by the globular C-terminal domain. Ligands binding to the N-terminal domain abolish the spontaneous ionic currents associated with neurotoxic mutants of PrP, and the isolated N-terminal domain induces currents when expressed in the absence of the C-terminal domain.