Optical coherence tomography using physical domain data compression to achieve MHz A-scan rates
OPTICS EXPRESS
Authors: Stroud, Jasper R.; Liu, Luoluo; Chin, Sang; Tran, Trac D.; Foster, Mark A.
Abstract
The three-dimensional volumetric imaging capability of optical coherence tomography (OCT) leads to the generation of large amounts of data, which necessitates high speed acquisition followed by high dimensional image processing and visualization. This signal acquisition and processing pipeline demands high A-scan rates on the front end, which has driven researchers to push A-scan acquisition rates into the MHz regime. To this end, the optical time-stretch approach uses a mode locked laser (MLL) source, dispersion in optical fiber, and a single analog-to-digital converter (ADC) to achieve multi-MHz A-scan rates. While enabling impressive performance this Nyquist sampling approach is ultimately constrained by the sampling rate and bandwidth of the ADC. Additionally such an approach generates massive amounts of data. Here we present a compressed sensing (CS) OCT system that uses a MLL, electro-optic modulation, and optical dispersion to implement data compression in the physical domain and rapidly acquire real-time compressed measurements of the OCT signals. Compression in the analog domain prior to digitization allows for the use of lower bandwidth ADCs, which reduces cost and decreases the required data capacity of the sampling interface. By leveraging a compressive A-scan optical sampling approach and the joint sparsity of C-scan data we demonstrate 14.4-MHz to 144-MHz A-scan acquisition speeds using a sub-Nyquist 1.44 Gsample/sec ADC sampling rate. Furthermore we evaluate the impact of data compression and resulting imaging speed on image quality. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
H2B ubiquitylation enhances H3K4 methylation activities of human KMT2 family complexes
NUCLEIC ACIDS RESEARCH
Authors: Kwon, Minjung; Park, Kihyun; Hyun, Kwangbeom; Lee, Jeong-Heon; Zhou, Linjiao; Cho, Young-Wook; Ge, Kai; Skalnik, David G.; Muir, Tom W.; Kim, Jaehoon
Abstract
In mammalian cells, distinct H3K4 methylation states are created by deposition of methyl groups by multiple complexes of histone lysine methyltransferase 2 (KMT2) family proteins. For comprehensive analyses that directly compare the catalytic properties of all six human KMT2 complexes, we employed a biochemically defined system reconstituted with recombinant KMT2 core complexes (KMT2(Core)Cs) containing minimal components required for nucleosomal H3K4 methylation activity. We found that each KMT2(Core)C generates distinct states and different levels of H3K4 methylation, and except for MLL3 all are stimulated by H2Bub. Notably, SET1B(Core)C exhibited the strongest H3K4 methylation activity and, to our surprise, did not require H2B ubiquitylation (H2Bub); in contrast, H2Bub was required for the H3K4me2/3 activity of the paralog SET1A(Core)C. We also found that WDR5, RbBP5, ASH2L and DPY30 are required for efficient H3K4 methyltransferase activities of all KMT2(Core)Cs except MLL3, which could produce H3K4me1 in the absence of WDR5. Importantly, deletion of the PHD2 domain of CFP1 led to complete loss of the H3K4me2/3 activities of SET1A/(BCs)-Cs-Core in the presence of H2Bub, indicating a critical role for this domain in the H2Bub-stimulated H3K4 methylation. Collectively, our results suggest that each KMT2 complex methylates H3K4 through distinct mechanisms in which individual subunits differentially participate.