Sensitive optical biosensors for unlabeled targets: a review.

Functional genomics reveal that the serine synthesis pathway is essential in breast cancer

Nucleotides are required for a wide variety of biological processes and are constantly synthesized de novo in all cells. When cells proliferate, increased nucleotide synthesis is necessary for DNA replication and for RNA production to support protein synthesis at different stages of the cell cycle, during which these events are regulated at multiple levels. Therefore the synthesis of the precursor nucleotides is also strongly regulated at multiple levels. Nucleotide synthesis is an energy intensive process that uses multiple metabolic pathways across different cell compartments and several sources of carbon and nitrogen. The processes are regulated at the transcription level by a set of master transcription factors but also at the enzyme level by allosteric regulation and feedback inhibition. Here we review the cellular demands of nucleotide biosynthesis, their metabolic pathways and mechanisms of regulation during the cell cycle. The use of stable isotope tracers for delineating the biosynthetic routes of the multiple intersecting pathways and how these are quantitatively controlled under different conditions is also highlighted. Moreover, the importance of nucleotide synthesis for cell viability is discussed and how this may lead to potential new approaches to drug development in diseases such as cancer.

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Regulation of mammalian nucleotide metabolism and biosynthesis

Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates

Methods of manufacturing a liquid crystal device including depositing a layer of liquid crystal material on a substrate and imprinting a pattern on the layer of liquid crystal material using an imprint template are disclosed. The liquid crystal material can be jet deposited. The imprint template can include surface relief features, Pancharatnam-Berry Phase Effect (PBPE) structures or diffractive structures. The liquid crystal device manufactured by the methods described herein can be used to manipulate light, such as for beam steering, wavefront shaping, separating wavelengths and/or polarizations, and combining different wavelengths and/or polarizations.

Virtual and augmented reality systems and methods

A high sensitivity plastic biosensor based on detection of changes in optical density on the surface of a narrow bandwidth guided mode resonant filter is demonstrated. Using sub-micron microreplication of a master sensor surface structure on continuous sheets of plastic film, the sensor can be produced inexpensively over large surface areas. In this work, the sensor structure is incorporated into standard 96-well microtiter plates and used to perform a protein–protein affinity assay. A surface receptor immobilization protocol demonstrating low nonspecific binding is used to detect an antibody with 8.3 nM sensitivity. By measuring the kinetic interaction of a protein–protein binding pair simultaneously at several concentrations, the affinity binding constant can be quickly determined.

A plastic colorimetric resonant optical biosensor for multiparallel detection of label-free biochemical interactions

Methods and compositions are provided for detecting biomolecular interactions. The use of labels is not required and the methods can be performed in a high-throughput manner. The invention also provides optical devices useful as narrow band filters.

Optical detection of label-free biomolecular interactions using microreplicated plastic sensor elements

Autophagy is an important cellular catabolic process that plays a variety of important roles, including maintenance of the amino acid pool during starvation, recycling of damaged proteins and organelles, and clearance of intracellular microbes. Currently employed autophagy detection methods include fluorescence microscopy, biochemical measurement, SDS-PAGE and western blotting, but they are time consuming, labor intensive, and require much experience for accurate interpretation. More recently, development of novel fluorescent probes have allowed the investigation of autophagy via standard flow cytometry. However, flow cytometers remain relatively expensive and require a considerable amount of maintenance. Previously, image-based cytometry has been shown to perform automated fluorescence-based cellular analysis comparable to flow cytometry. In this study, we developed a novel method using the Cellometer image-based cytometer in combination with Cyto-ID® Green dye for autophagy detection in live cells. The ...

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A novel image-based cytometry method for autophagy detection in living cells

Guided mode resonant filter biosensor using a linear grating surface structure

Although cells require nutrients to proliferate, most nutrient exchange rates of the NCI60 panel of cancer cell lines correlate poorly with their proliferation rate. Here, we provide evidence indicating that this inconsistency is rooted in the variability of cell size. We integrate previously reported data characterizing genome copy number variations, gene expression, protein expression and exchange fluxes with our own measurements of cell size and protein content in the NCI60 panel of cell lines. We show that protein content, DNA content, and protein synthesis per cell are proportional to the cell volume, and that larger cells proliferate slower than smaller cells. We estimate the metabolic fluxes of these cell lines and show that their magnitudes are proportional to their protein synthesis rate and, after correcting for cell volume, to their proliferation rate. At the level of gene expression, we observe that genes expressed at higher levels in smaller cells are enriched for genes involved in cell cycle, while genes expressed at higher levels in large cells are enriched for genes expressed in mesenchymal cells. The latter finding is further corroborated by the induction of those same genes following treatment with TGFβ, and the high vimentin but low E-cadherin protein levels in the larger cells. We also find that aromatase inhibitors, statins and mTOR inhibitors preferentially inhibit the in vitro growth of cancer cells with high protein synthesis rates per cell. The NCI60 cell lines display various metabolic activities, and the type of metabolic activity that they possess correlates with their cell volume and protein content. In addition to cell proliferation, cell volume and/or biomarkers of protein synthesis may predict response to drugs targeting cancer metabolism.

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Jean Qiu

Papers

A plastic colorimetric resonant optical biosensor for multiparallel detection of label-free biochemical interactions

Optical detection of label-free biomolecular interactions using microreplicated plastic sensor elements

A novel image-based cytometry method for autophagy detection in living cells

Guided mode resonant filter biosensor using a linear grating surface structure

The metabolic demands of cancer cells are coupled to their size and protein synthesis rates