We present a robust and general shotgun glycoproteomics approach to comprehensively profile glycoproteins in complex biological mixtures. In this approach, glycopeptides derived from glycoproteins are enriched by selective capture onto a solid support using hydrazide chemistry followed by enzymatic release of the peptides and subsequent analysis by tandem mass spectrometry. The approach was validated using standard protein mixtures that resulted in a close to 100% capture efficiency. Our capture approach was then applied to microsomal fractions of the cisplatinresistant ovarian cancer cell line IGROV-1/CP. With a Protein Prophet probability value greater than 0.9, we identified a total of 302 proteins with an average protein identification rate of 136 ؎ 19 (n ‫؍‬ 4) in a single linear quadrupole ion trap (LTQ) mass spectrometer nano-LC-MS experiment and a selectivity of 91 ؎ 1.6% (n ‫؍‬ 4) for the N-linked glycoconsensus sequence. Our method has several advantages. 1) Digestion of proteins initially into peptides improves the solubility of large membrane proteins and exposes all of the glycosylation sites to ensure equal accessibility to capture reagents. 2) Capturing glycosylated peptides can effectively reduce sample complexity and at the same time increase the confidence of MS-based protein identifications (more potential peptide identifications per protein). 3) The utility of sodium sulfite as a quencher in our capture approach to replace the solid phase extraction step in an earlier glycoprotein chemical capture approach for removing excess sodium periodate allows the overall capture procedure to be completed in a single vessel. This improvement minimizes sample loss, increases sensitivity, and makes our protocol amenable for high throughput implementation, a feature that is essential for biomarker identification and validation of a large number of clinical samples. 4) The approach is demonstrated here on the analysis of N-linked glycopeptides; however, it can be applied equally well to

This paper describes a new method to measure the encapsulation efficiency of individual lipid vesicles. Single vesicles were first optically trapped (with a CW Nd:YAG laser at 1064 nm) and then photolyzed with a single 3-ns UV laser pulse (from a N(2) laser at 337 nm) to release the molecules encapsulated within the vesicle; confocal detection with single-molecule sensitivity (laser excitation at 488 nm from a CW Ar(+) laser) was used to measure the number of released molecules. By placing the confocal probe volume a few micrometers from the vesicle and by monitoring the transit times and the number of released molecules that crossed this probe volume, we could calculate the total number of molecules released from the vesicle using a three-dimensional diffusion equation. Unlike traditional definitions of encapsulation efficiencies based on bulk assays, because we can measure the contents of and release from individual vesicles, we can define the encapsulation efficiency by dividing the concentration of molecules encapsulated in each vesicle over the original concentration of the molecules present in the loading solution. We characterized the encapsulation efficiency of carboxyfluorescein for vesicles prepared by rotary evaporation and found oligolamellar vesicles have an encapsulation efficiency of 36.3 +/- 18.9%, while multilamellar vesicles have an encapsulation efficiency of 17.5 +/- 8.9%.

This paper demonstrates the ability to grow silica directly on a deposited surface of polyelectrolyte. Using this strategy, we describe the deposition of layered polyelectrolyte-silica coating on negatively charged surfaces of polystyrene particles and latex nanocapsules, which could not be coated directly with silica alone. By etching away the underlying polystyrene bead, we were able to form polyelectrolyte-silica capsules that were mechanically robust. Using scanning and transmission electron microscopy, we imaged and studied the coating after the deposition of each layer of polyelectrolyte and silica. We then applied this new coating to latex nanocapsules that were loaded with fluorescein molecules. We found that the coating procedure did not cause the loaded molecules to leak out from the capsules, and we determined that the variation in the number of loaded molecules among capsules arose from differences in the volume of the nanocavities and was not caused by the loading and coating of the capsules. This layered architecture permits the thickness of the coating to be controlled in principle over a wide dynamic range, but more importantly, this coating could act as an effective seal to prevent undesired leakage from nanocapsules and thus increase the long-term storability of loaded capsules. Over a 30-day period, we determined that leakage from uncoated capsules was significant but negligible for ones that were coated with two layers of polyelectrolyte-silica. Using single-pulse UV photolysis of individual nanocapsules, we demonstrate that the molecules contained within coated capsules could be released effectively and on demand with a single laser pulse.

The searching of human housekeeping (HK) genes has been a long quest since the emergence of transcriptomics, and is instrumental for us to understand the structure of genome and the fundamentals of biological processes. The resolved genes are frequently used in evolution studies and as normalization standards in quantitative gene-expression analysis. Within the past 20 years, more than a dozen HK-gene studies have been conducted, yet none of them sampled human tissues completely. We believe an integration of these results will help remove false positive genes owing to the inadequate sampling. Surprisingly, we only find one common gene across 15 examined HK-gene datasets comprising 187 different tissue and cell types. Our subsequent analyses suggest that it might not be appropriate to rigidly define HK genes as expressed in all tissue types that have diverse developmental, physiological, and pathological states. It might be beneficial to use more robustly identified HK functions for filtering criteria, in which the representing genes can be a subset of genome. These genes are not necessarily the same, and perhaps need not to be the same, everywhere in our body.

This paper describes the synthesis and loading of silica and polystyrene-acrylic based nanocapsules with small molecules. The nanocapsules are used for delivering defined packages of stimuli to single cells with both high spatial and temporal resolutions. To introduce molecules into the capsules, we characterized two approaches. The first approach is based on a base-swell process in which the shell of the capsule is swelled so small molecules can diffuse into the interior of the capsule and be trapped inside once the capsules are de-swelled. The second approach is based on a dry-swell-dry process in which the solution containing the molecules of interest and the nanocapsules is physically dried to promote more molecules to enter into the interior of the capsule. We characterized both methods by monitoring the content of and the release from individual capsules with confocal microscopy and wide-field imaging. To illustrate the biological applications of such nanocapsules, we used optical trapping to position a single carbachol-loaded capsule adjacent to a single CHO cell that has been transfected with muscarinic acetylcholine (M1) receptors, released the carbachol from the capsule with a single 3-ns N2 laser pulse, and then monitored the subsequent intracellular signaling triggered by the binding of carbachol to the M1 receptors.