Measurement of replication structures at the nanometer scale using super-resolution light microscopy.

DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells.

Mechanisms of polarization switching in single-transverse-mode vertical-cavity surface-emitting lasers: thermal shift and nonlinear semiconductor dynamics.

We analyze polarization switching in vertical-cavity surface-emitting lasers, taking into account a proper semiconductor frequency-dependent complex susceptibility and spin-flip processes. Thermal effects are included as a varying detuning, and gain differences arise from birefringence splitting. We find that, for large birefringence, gain differences between the two linearly polarized modes are preponderant, and switching occurs owing to thermal shift.

Targeting and tracing antigens in live cells with fluorescent nanobodies.

We fused the epitope-recognizing fragment of heavy-chain antibodies from Camelidae sp. with fluorescent proteins to generate fluorescent, antigen-binding nanobodies (chromobodies) that can be expressed in living cells. We demonstrate that chromobodies can recognize and trace antigens in different subcellular compartments throughout S phase and mitosis.

CPT1alpha over-expression increases long-chain fatty acid oxidation and reduces cell viability with incremental palmitic acid concentration in 293T cells.

To test the cellular response to an increased fatty acid oxidation, we generated a vector for an inducible expression of the rate-limiting enzyme carnitine palmitoyl-transferase 1alpha (CPT1alpha). Human embryonic 293T kidney cells were transiently transfected and expression of the CPT1alpha transgene in the tet-on vector was activated with doxycycline. Fatty acid oxidation was measured by determining the conversion of supplemented, synthetic cis-10-heptadecenoic acid (C17:1n-7) to C15:ln-7.

DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters.

The spatial and temporal organization of DNA replication was investigated in living cells with a green fluorescent protein fusion to the DNA polymerase clamp PCNA. In situ extractions and photobleaching experiments revealed that PCNA, unlike RPA34, shows little if any turnover at replication sites, suggesting that it remains associated with the replication machinery through multiple rounds of Okazaki fragment synthesis. Photobleaching analyses further showed that the transition from earlier to later replicons occurs by disassembly into a nucleoplasmic pool of rapidly diffusing subcomponents and reassembly at newly activated sites.