Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii

Intraflagellar transport moves proteins in and out of flagella/cilia and it is essential for the assembly of these organelles. Using whole-genome sequencing, we identified splice site mutations in two IFT genes, IFT81 ( fla9 ) and IFT121 ( ift121-2 ), which lead to flagellar assembly defects in the unicellular green alga Chlamydomonas reinhardtii . The splicing defects in these ift mutants are partially corrected by mutations in two conserved spliceosome proteins, DGR14 and FRA10. We identified a dgr14 deletion mutant, which suppresses the 3′ splice site mutation in IFT81 , and a frameshift mutant of FRA10 , which suppresses the 5′ splice site mutation in IFT121 . Surprisingly, we found dgr14-1 and fra10 mutations suppress both splice site mutations. We suggest these two proteins are involved in facilitating splice site recognition/interaction; in their absence some splice site mutations are tolerated. Nonsense mutations in SMG1 , which is involved in nonsense-mediated decay, lead to accumulation of aberrant transcripts and partial restoration of flagellar assembly in the ift mutants. The high density of introns and the conservation of noncore splicing factors, together with the ease of scoring the ift mutant phenotype, make Chlamydomonas an attractive organism to identify new proteins involved in splicing through suppressor screening. </jats:p

Quincke Oscillators: Dynamics, synchronization, and assembly of self-oscillating colloids

Active colloids are small particles that can convert external energy supply into self-propulsion. Because of the existence of the energy current inside and across the system, active colloids exhibit behaviors that are far away from thermodynamic equilibrium. During the past decades, active colloids have been used to provide models for many different non-equilibrium system studies and have been designed to complete tasks on small scale. By tuning the particle size, shape, etc, or changing the actuation methods of the active colloid systems, people have developed a large number of different active colloid systems. Among all active colloid systems, the Quincke rotation system can effectively propel particles with rapid speed. This phenomenon refers to the spontaneous rolling of a dielectric sphere in a weakly conducting liquid under a DC electric field. Although the basic mechanism of a single Quincke roller has been well explained, some behaviors that occur in complex environments or with multiple Quincke particles are still mysteries. For example, one particle will move back and forth on the bottom electrode under a high electric DC field. This so-called Quincke Oscillation motion cannot be explained by the previous models well. So a new model is required. In this dissertation, we will focus on explaining this newly-discovered dynamic in the Quincke system. Then we will study the collective dynamics of multiple Quincke oscillators with designed experiments and models. In Chapter 1, the background and different actuation methods of active colloid systems are first introduced. Then the Quincke rotation system and its field-dependent dynamics are explained with a classic leaky dielectric model. The recent research results with Quincke systems are shortly reviewed afterward. In Chapter 2, we introduce the experimentally discovered Quincke Oscillation phenomenon. Then we reveal its dependency on liquid conductivity and particle size. This dynamic is finally explained by the asymmetric charging of the particle surface in the field-induced boundary layer near the electrode. This work opens the door to the study of the collective dynamics of Quincke oscillators. In Chapter 3, we first introduce a dynamical model considering the charge, dipole, and quadrupole moments of the sphere and predict its oscillatory motion under a non-uniform liquid conductivity environment. Then we study the behavior of two coupled Quincke oscillators with far-field hydrodynamic and electrostatic interactions. The numerical simulations predict the synchronization and alignment of two oscillators with fixed positions. We further develop a model based on weakly coupled oscillator assumptions by considering the relative phase and oscillating orientations of two oscillators. The model successfully explains the numerical simulation results and can be applied to other active colloid systems with multiple mobile oscillators. In Chapter 4, we show that the Quincke oscillators can assemble into a cluster and oscillate with high synchronization and alignment. This formation of the cluster can also increase the oscillation frequency of the oscillators. By considering the perfect contact rolling of the oscillators on the electrode, we develop a weakly coupled oscillator theory model. This model explains the tendency of particles to synchronize and align in a cluster and predicts the increase of the oscillation frequency when particles are in synchronized phases. The cluster is stabilized due to the existing phase waves observed in experiments and simulations. In Chapter 5, we introduce two other studies on Quincke rollers with different experimental designs. Particles of helical shape exhibit self-propulsion in the liquid bulk and highlight the role of shape in controlling particle dynamics. For multiple spheres in a height-confined system, the particles display a transition from a fluctuating state to an absorbing stable state depending on their density and the applied field strength. This work provides an experimental model for studying absorbing state. In Chapter 6, the development of the Quincke system study is reviewed and some future directions are suggested

Organization of the human intestine at single-cell resolution

The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall healt

Anisotropic Generalized Bayesian Coherent Point Drift for Point Set Registration

Registration is highly demanded in many real-world scenarios such as robotics and automation. Registration is challenging partly due to the fact that the acquired data is usually noisy and has many outliers. In addition, in many practical applications, one point set (PS) usually only covers a partial region of the other PS. Thus, most existing registration algorithms cannot guarantee theoretical convergence. This article presents a novel, robust, and accurate three-dimensional (3D) rigid point set registration (PSR) method, which is achieved by generalizing the state-of-the-art (SOTA) Bayesian coherent point drift (BCPD) theory to the scenario that high-dimensional point sets (PSs) are aligned and the anisotropic positional noise is considered. The high-dimensional point sets typically consist of the positional vectors and normal vectors. On one hand, with the normal vectors, the proposed method is more robust to noise and outliers, and the point correspondences can be found more accurately. On the other hand, incorporating the registration into the BCPD framework will guarantee the algorithm's theoretical convergence. Our contributions in this article are three folds. First, the problem of rigidly aligning two general PSs with normal vectors is incorporated into a variational Bayesian inference framework, which is solved by generalizing the BCPD approach while the anisotropic positional noise is considered. Second, the updated parameters during the algorithm's iterations are given in closed-form or with iterative solutions. Third, extensive experiments have been done to validate the proposed approach and its significant improvements over the BCPD

Study on Spatial Distribution of Soil Available Microelement in Qujing Tobacco Farming Area, China

AbstractDescriptive analysis characteristics and spatial variation characteristics of soil available microelements were studied based on SPSS and GIS Soil available microelements spatial distribution maps were created with ordinary Kriging method. The results indicate that, 7 available microelements in tobacco soil obey lognormal distribution, all the available microelements were intermediate variability; Anisotropic structure of available microelements of tobacco soil varies evidently, spatial variability of available B was mainly caused by random factors, and others’ spatial variability were caused by structural factors and random factors; Spatial distribution maps show that, available B was widely deficient in tobacco soil of Qujing farming area, ‘lower level’ and ‘low level’ taken 7.74% and 68.20%, respectively available Zn distribution was moderate, only 1.32% of the area lack of Zn, available Cu, available Fe and available Mn were extremely high in the whole extension, available Mo was deficient in part of the region with 28.38%, water soluble Cl was higher than critical value(30mgkg−1)in the most of Qujing farming area, which taken 38.86%

Reliable Hybrid Mixture Model for Generalized Point Set Registration

Point set registration (PSR) is an essential problem in the field of surgical navigation and augmented reality (AR). In surgical navigation, the aim of registration is mapping the pre-operative space to the intra-operative space. This article introduces a reliable hybrid mixture model, in which the reliability of the normal vectors in the generalized point set (GPS) is examined and exploited. The motivation of considering the reliability of orientation information is that normal vectors cannot be estimated or measured accurately in the clinic. The point set (PS) is divided into two subsets according to the reliability of normal vectors. PSR is cast into the maximum likelihood estimation (MLE) problem. The expectation maximization (EM) framework is used to solve the MLE problem. In the E-step, the posterior probabilities between points in two PSs are computed. In the M-step, the transformation matrix and model components are updated by optimizing the objective function. We have demonstrated through extensive experiments on the human femur bone PS that the proposed algorithm outperforms the state-of-the-art ones in terms of accuracy, robustness, and convergence speed