Attempting to distinguish between endogenous and contaminating cytokeratins in a corneal proteomic study

<p>Abstract</p> <p>Background</p> <p>The observation of cytokeratins (CK's) in mass spectrometry based studies raises the question of whether the identified CK is a true endogenous protein from the sample or simply represents a contaminant. This issue is especially important in proteomic studies of the corneal epithelium where several CK's have previously been reported to mark the stages of differentiation from corneal epithelial stem cell to the differentiated cell.</p> <p>Methods</p> <p>Here we describe a method to distinguish very likely endogenous from uncertain endogenous CK's in a mass spectrometry based proteomic study. In this study the CK identifications from 102 human corneal samples were compared with the number of human CK identifications found in 102 murine thymic lymphoma samples.</p> <p>Results</p> <p>It was anticipated that the CK's that were identified with a frequency of <5%, <it>i.e. </it>in less than one spot for every 20 spots analysed, are very likely to be endogenous and thereby represent a 'biologically significant' identification. CK's observed with a frequency >5% are uncertain endogenous since they may represent true endogenous CK's but the probability of contamination is high and therefore needs careful consideration. This was confirmed by comparison with a study of mouse samples where all identified human CK's are contaminants.</p> <p>Conclusions</p> <p>CK's 3, 4, 7, 8, 11, 12, 13, 15, 17, 18, 19, 20 and 23 are very likely to be endogenous proteins if identified in a corneal study, whilst CK's 1, 2e, 5, 6A, 9, 10, 14 and 16 may be endogenous although some are likely to be contaminants in a proteomic study. Further immunohistochemical analysis and a search of the current literature largely supported the distinction.</p

Boundary stress-energy tensor and Newton-Cartan geometry in Lifshitz holography

For a specific action supporting z = 2 Lifshitz geometries we identify the Lifshitz UV completion by solving for the most general solution near the Lifshitz boundary. We identify all the sources as leading components of bulk fields which requires a vielbein formalism. This includes two linear combinations of the bulk gauge field and timelike vielbein where one asymptotes to the boundary timelike vielbein and the other to the boundary gauge field. The geometry induced from the bulk onto the boundary is a novel extension of Newton-Cartan geometry that we call torsional Newton-Cartan (TNC) geometry. There is a constraint on the sources but its pairing with a Ward identity allows one to reduce the variation of the on-shell action to unconstrained sources. We compute all the vevs along with their Ward identities and derive conditions for the boundary theory to admit conserved currents obtained by contracting the boundary stress-energy tensor with a TNC analogue of a conformal Killing vector. We also obtain the anisotropic Weyl anomaly that takes the form of a Hořava-Lifshitz action defined on a TNC geometry. The Fefferman-Graham expansion contains a free function that does not appear in the variation of the on-shell action. We show that this is related to an irrelevant deformation that selects between two different UV completions