The influence of coiled-coil motif of serine recombinase toward the directionality regulation.

Serine integrases promote the recombination of two complementary DNA sequences, attP and attB, to create hybrid sequences, attL and attR. The reaction is unidirectional in the absence of an accessory protein called recombination directionality factor. We utilized tethered particle motion (TPM) experiments to investigate the reaction behaviors of two model serine integrases from Listeria innocua phage LI and Streptomyces coelicolor phage C31. Detailed kinetic analyses of wild-type and mutant proteins were carried out to verify the mechanisms of recombination directionality. In particular, we assessed the influence of a coiled-coil motif (CC) that is conserved in the C-terminal domain of serine integrases and is an important prerequisite for efficient recombination. Compared to wild type, we found that CC deletions in both serine integrases reduced the overall abundance of integrase (Int) att-site complexes and favored the formation of nonproductive complexes over recombination-competent complexes. Furthermore, the rate at which CC mutants formed productive synaptic complexes and disassembled aberrant nonproductive complexes was significantly reduced. It is notable that while the φC31 Int CC is essential for recombination, the LI Int CC plays an auxiliary role for recombination to stabilize protein-protein interactions and to control the directionality of the reaction.

Non-Invasive Heart Rate Estimation From Ballistocardiograms Using Bidirectional LSTM Regression.

Non-invasive heart rate estimation is of great importance in daily monitoring of cardiovascular diseases. In this paper, a bidirectional long short term memory (bi-LSTM) regression network is developed for non-invasive heart rate estimation from the ballistocardiograms (BCG) signals. The proposed deep regression model provides an effective solution to the existing challenges in BCG heart rate estimation, such as the mismatch between the BCG signals and ground-truth reference, multi-sensor fusion and effective time series feature learning. Allowing label uncertainty in the estimation can reduce the manual cost of data annotation while further improving the heart rate estimation performance. Compared with the state-of-the-art BCG heart rate estimation methods, the strong fitting and generalization ability of the proposed deep regression model maintains better robustness to noise (e.g., sensor noise) and perturbations (e.g., body movements) in the BCG signals and provides a more reliable solution for long term heart rate monitoring.

A bipartite thermodynamic-kinetic contribution by an activating mutation to RDF-independent excision by a phage serine integrase.

Streptomyces phage ϕC31 integrase (Int)-a large serine site-specific recombinase-is autonomous for phage integration (attP x attB recombination) but is dependent on the phage coded gp3, a recombination directionality factor (RDF), for prophage excision (attL x attR recombination). A previously described activating mutation, E449K, induces Int to perform attL x attR recombination in the absence of gp3, albeit with lower efficiency. E449K has no adverse effect on the competence of Int for attP x attB recombination. Int(E449K) resembles Int in gp3 mediated stimulation of attL x attR recombination and inhibition of attP x attB recombination. Using single-molecule analyses, we examined the mechanism by which E449K activates Int for gp3-independent attL x attR recombination. The contribution of E449K is both thermodynamic and kinetic. First, the mutation modulates the relative abundance of Int bound attL-attR site complexes, favoring pre-synaptic (PS) complexes over non-productively bound complexes. Roughly half of the synaptic complexes formed from Int(E449K) pre-synaptic complexes are recombination competent. By contrast, Int yields only inactive synapses. Second, E449K accelerates the dissociation of non-productively bound complexes and inactive synaptic complexes formed by Int. The extra opportunities afforded to Int(E499K) in reattempting synapse formation enhances the probability of success at fruitful synapsis.

A Flp-SUMO hybrid recombinase reveals multi-layered copy number control of a selfish DNA element through post-translational modification.

Mechanisms for highly efficient chromosome-associated equal segregation, and for maintenance of steady state copy number, are at the heart of the evolutionary success of the 2-micron plasmid as a stable multi-copy extra-chromosomal selfish DNA element present in the yeast nucleus. The Flp site-specific recombination system housed by the plasmid, which is central to plasmid copy number maintenance, is regulated at multiple levels. Transcription of the FLP gene is fine-tuned by the repressor function of the plasmid-coded partitioning proteins Rep1 and Rep2 and their antagonist Raf1, which is also plasmid-coded. In addition, the Flp protein is regulated by the host's post-translational modification machinery. Utilizing a Flp-SUMO fusion protein, which functionally mimics naturally sumoylated Flp, we demonstrate that the modification signals ubiquitination of Flp, followed by its proteasome-mediated degradation. Furthermore, reduced binding affinity and cooperativity of the modified Flp decrease its association with the plasmid FRT (Flp recombination target) sites, and/or increase its dissociation from them. The resulting attenuation of strand cleavage and recombination events safeguards against runaway increase in plasmid copy number, which is deleterious to the host-and indirectly-to the plasmid. These results have broader relevance to potential mechanisms by which selfish genomes minimize fitness conflicts with host genomes by holding in check the extra genetic load they pose.

Monitoring the Relative Blood Pressure Using a Hydraulic Bed Sensor System.

We propose a nonwearable hydraulic bed sensor system that is placed underneath the mattress to estimate the relative systolic blood pressure of a subject, which only differs from the actual blood pressure by a scaling and an offset factor. Two types of features are proposed to obtain the relative blood pressure, one based on the strength and the other on the morphology of the bed sensor ballistocardiogram pulses. The relative blood pressure is related to the actual by a scale and an offset factor that can be obtained through calibration. The proposed system is able to extract the relative blood pressure more accurately with a less sophisticated sensor system compared to those from the literature. We tested the system using a dataset collected from 48 subjects right after active exercises. Comparison with the ground truth obtained from the blood pressure cuff validates the promising performance of the proposed system, where the mean correlation between the estimate and the ground truth is near to 90% for the strength feature and 83% for the morphology feature.

The synergy between RSC, Nap1 and adjacent nucleosome in nucleosome remodeling.

Eukaryotes have evolved a specific strategy to package DNA. The nucleosome is a 147-base-pair DNA segment wrapped around histone core proteins that plays important roles regulating DNA-dependent biosynthesis and gene expression. Chromatin remodeling complexes (RSC, Remodel the Structure of Chromatin) hydrolyze ATP to perturb DNA-histone contacts, leading to nucleosome sliding and ejection. Here, we utilized tethered particle motion (TPM) experiments to investigate the mechanism of RSC-mediated nucleosome remodeling in detail. We observed ATP-dependent RSC-mediated DNA looping and nucleosome ejection along individual mononucleosomes and dinucleosomes. We found that nucleosome assembly protein 1 (Nap1) enhanced RSC-mediated nucleosome ejection in a two-step disassembly manner from dinucleosomes but not from mononucleosomes. Based on this work, we provide an entire reaction scheme for the RSC-mediated nucleosome remodeling process that includes DNA looping, nucleosome ejection, the influence of adjacent nucleosomes, and the coordinated action between Nap1 and RSC.

Multiple Instance Dictionary Learning for Beat-to-Beat Heart Rate Monitoring From Ballistocardiograms.

A multiple instance dictionary learning approach, dictionary learning using functions of multiple instances (DL-FUMI), is used to perform beat-to-beat heart rate estimation and to characterize heartbeat signatures from ballistocardiogram (BCG) signals collected with a hydraulic bed sensor. DL-FUMI estimates a "heartbeat concept" that represents an individual's personal ballistocardiogram heartbeat pattern. DL-FUMI formulates heartbeat detection and heartbeat characterization as a multiple instance learning problem to address the uncertainty inherent in aligning BCG signals with ground truth during training. Experimental results show that the estimated heartbeat concept obtained by DL-FUMI is an effective heartbeat prototype and achieves superior performance over comparison algorithms.

Robust heartbeat detection from in-home ballistocardiogram signals of older adults using a bed sensor.

We propose a simple and robust method to detect heartbeats using the ballistocardiogram (BCG) signal that is produced by a hydraulic bed sensor placed under the mattress. The proposed method is found beneficial especially when the BCG signal does not display consistent J-peaks, which can often be the case for overnight, in-home monitoring, especially with frail seniors. Heartbeat detection is based on the short-time energy of the BCG signal. Compared with previous methods that rely on the J-peaks observed from the BCG amplitude, we are able to achieve considerable improvement even when significant distortions are present. Test results are included for different BCG waveform patterns from older adults.

Doppler radar fall activity detection using the wavelet transform.

We propose in this paper the use of Wavelet transform (WT) to detect human falls using a ceiling mounted Doppler range control radar. The radar senses any motions from falls as well as nonfalls due to the Doppler effect. The WT is very effective in distinguishing the falls from other activities, making it a promising technique for radar fall detection in nonobtrusive inhome elder care applications. The proposed radar fall detector consists of two stages. The prescreen stage uses the coefficients of wavelet decomposition at a given scale to identify the time locations in which fall activities may have occurred. The classification stage extracts the time-frequency content from the wavelet coefficients at many scales to form a feature vector for fall versus nonfall classification. The selection of different wavelet functions is examined to achieve better performance. Experimental results using the data from the laboratory and real inhome environments validate the promising and robust performance of the proposed detector.