ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR.

Motivation: Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the bisulfite sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP.

Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy.

Living cells use signaling and regulatory mechanisms to adapt to environmental stresses. Adaptation to oxidative stress involves the regulation of many enzymes in both glycolysis and pentose phosphate pathways (PPP), so as to support PPP-driven NADPH recycling for antioxidant defense. The underlying regulatory logic is investigated by developing a kinetic modeling approach fueled with metabolomics and C-fluxomics datasets from human fibroblast cells.

Protein level variability determines phenotypic heterogeneity in proteotoxic stress response.

Cell-to-cell variability in stress response is a bottleneck for the construction of accurate and predictive models which could guide clinical diagnosis and treatment of certain diseases, for example, cancer. Indeed, such phenotypic heterogeneity can lead to fractional killing and persistence of a subpopulation of cells which are resistant to a given treatment. The heat shock response network plays a major role in protecting the proteome against several types of injuries.

Transcriptomic Analysis of Breast Cancer Stem Cells and Development of a pALDH1A1:mNeptune Reporter System for Live Tracking.

Many solid cancers are hierarchically organized with a small number of cancer stem cells (CSCs) able to regrow a tumor, while their progeny lacks this feature. Breast CSC is known to contribute to therapy resistance. The study of those cells is usually based on their cell-surface markers like CD44 /CD24 or their aldehyde dehydrogenase (ALDH) activity.

Bacterial Chemoreceptor Imaging at High Spatiotemporal Resolution Using Photoconvertible Fluorescent Proteins.

We describe two methods for high-resolution fluorescence imaging of the positioning and mobility of E. coli chemoreceptors fused to photoconvertible fluorescent proteins. Chemoreceptors such as Tar and Tsr are transmembrane proteins expressed at high levels (thousands of copies per cell).

Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET.

We present single-cell FRET measurements in the chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations.

Cancerous cell death from sensitizer free photoactivation of singlet oxygen.

Singlet oxygen ((1)O(2)) is an electronic state of molecular oxygen which plays a major role in many chemical and biological photo-oxidation processes. It has a high chemical reactivity which is commonly harnessed for therapeutic issues. Indeed, (1)O(2) is believed to be the major cytotoxic agent in photodynamic therapy.

A high-power tunable Raman fiber ring laser for the investigation of singlet oxygen production from direct laser excitation around 1270 nm.

We report on the development of a tunable Raman fiber ring laser especially designed for the investigation of the 3Σ(-)(g) →1 Δg transition of molecular oxygen. Singlet oxygen (1Δg) is a reactive species of importance in the fields of biology, photochemistry, and phototherapy. Tunability of the Raman fiber ring laser is achieved without the use of an intracavity tunable bandpass filter and the laser thus achieves a slope efficiency only obtained up to now in Perot-Fabry cavities.