Molecular architecture of the kinetochore-microtubule attachment site is conserved between point and regional centromeres

Point and regional centromeres specify a unique site on each chromosome for kinetochore assembly. The point centromere in budding yeast is a unique 150-bp DNA sequence, which supports a kinetochore with only one microtubule attachment. In contrast, regional centromeres are complex in architecture, can be up to 5 Mb in length, and typically support many kinetochore-microtubule attachments. We used quantitative fluorescence microscopy to count the number of core structural kinetochore protein complexes at the regional centromeres in fission yeast and Candida albicans. We find that the number of CENP-A nucleosomes at these centromeres reflects the number of kinetochore-microtubule attachments instead of their length. The numbers of kinetochore protein complexes per microtubule attachment are nearly identical to the numbers in a budding yeast kinetochore. These findings reveal that kinetochores with multiple microtubule attachments are mainly built by repeating a conserved structural subunit that is equivalent to a single microtubule attachment site

GPR Image Noise Removal Using Grey Wolf Optimisation in the NSST Domain

Hyper-wavelet transforms, such as a non-subsampled shearlet transform (NSST), are one of the mainstream algorithms for removing random noise from ground-penetrating radar (GPR) images. Because GPR image noise is non-uniform, the use of a single fixed threshold for noisy coefficients in each sub-band of hyper-wavelet denoising algorithms is not appropriate. To overcome this problem, a novel NSST-based GPR image denoising grey wolf optimisation (GWO) algorithm is proposed. First, a time-varying threshold function based on the trend of noise changes in GPR images is proposed. Second, an edge area recognition and protection method based on the Canny algorithm is proposed. Finally, GWO is employed to select appropriate parameters for the time-varying threshold function and edge area protection method. The Natural Image Quality Evaluator is utilised as the optimisation index. The experiment results demonstrate that the proposed method provides excellent noise removal performance while protecting edge signals

Real-time measurement of nano-particle size using differential optical phase detection

We demonstrate a size sensing technique for nano-particles using optical differential phase measurement by a dual fiber interferometer through phase-generated carrier (PGC) demodulation. Nano-particle diameters are obtained from the differential phase shift as a result of adding an optical scattering perturbation into two-beam interference. Polystyrene nano-particles with diameters from 200 to 900 nm in a microfluidic channel are detected using this technique to acquire real-time particle diameters. Compared with amplitude sensing with over 10 mW of laser irradiance, particle sizing by PGC phase sensing can be achieved at a laser power as low as 1.18 mW. We further analyze major sources of noise in order to improve the limits of detection. This sensing technique may find a broad range of applications from the real-time selection of biological cell samples to rare cell detection in blood samples for early cancer screening.Published versio

Unsupervised SAR Despeckling by Combining Online Speckle Generation and Unpaired Training

Speckle suppression is a crucial preliminary step for synthetic aperture radar (SAR) image processing. Supervised despeckling approaches trained on synthetic datasets usually perform poorly in practice due to the unavailability of clean SAR images. Besides, the spatial correlation of speckle is rarely considered in many methods based on the fully developed speckle assumption. In this article, we propose an unsupervised despeckling method to address these issues by combining online speckle generation and unpaired training. The method consists of two branches: the stop-gradient branch and the unpaired branch. First, the stop-gradient branch learns to generate the spatially correlated speckle. Then, the unpaired branch combines the generated speckle with the unpaired optical image to form pairs of training data for network parameter updates. More specifically, in order to generate the more realistic speckle in the stop-gradient branch, we design a speckle correction module with three SAR speckle priors: the threshold prior, the unit mean prior, and the correlation prior coupled with the weighted patch-shuffle. In the unpaired training, a hybrid loss function is employed, which takes spatial smoothness and detail protection into consideration. Afterward, we combine the stop-gradient branch with the unpaired branch by the Siamese network to achieve alternate optimization of speckle generation and speckle removal. Finally, the optimization process in our method is analyzed theoretically. Qualitative and quantitative experiments demonstrate that the proposed method is comparable to the supervised despeckling approaches on synthetic datasets and outperforms several state-of-the-art unsupervised methods on real SAR datasets

A high-resolution map of nucleosome positioning on a fission yeast centromere

A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence