A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis

Ion homeostasis is essential for plant growth and environmental adaptation, and maintaining ion homeostasis requires the precise regulation of various ion transporters, as well as correct root patterning. However, the mechanisms underlying these processes remain largely elusive. Here, we reported that a choline transporter gene, CTL1, controls ionome homeostasis by regulating the secretory trafficking of proteins required for plasmodesmata (PD) development, as well as the transport of some ion transporters. Map-based cloning studies revealed that CTL1 mutations alter the ion profile of Arabidopsis thaliana. We found that the phenotypes associated with these mutations are caused by a combination of PD defects and ion transporter misregulation. We also established that CTL1 is involved in regulating vesicle trafficking and is thus required for the trafficking of proteins essential for ion transport and PD development. Characterizing choline transporter-like 1 (CTL1) as a new regulator of protein sorting may enable researchers to understand not only ion homeostasis in plants but also vesicle trafficking in general

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Topological valley transport of plate-mode waves in a homogenous thin plate with periodic stubbed surface

The study for exotic topological effects of sound has attracted uprising interests in fundamental physics and practical applications. Based on the concept of valley pseudospin, we demonstrate the topological valley transport of plate-mode waves in a homogenous thin plate with periodic stubbed surface, where a deterministic two-fold Dirac degeneracy is form by two plate modes. We show that the topological property can be controlled by the height of stubs deposited on the plate. By adjusting the relative heights of adjacent stubs, the valley vortex chirality and band inversion are induced, giving rise to a phononic analog of valley Hall phase transition. We further numerically demonstrate the valley states of plate-mode waves with robust topological protection. Our results provide a new route to design unconventional elastic topological insulators and will significantly broaden its practical application in the engineering field

Shannon entropy as an indicator of atomic avoided crossings for Rydberg potassium atoms interacting with a static electric field

We propose a method to calculate the positions of avoided crossings for Rydberg potassium in a static electric field by using Shannon entropy. Our method can be divided into two steps. At first we made a rough estimate of the range of the static electric field strength at which the given avoided crossings occur through strength dependence of the Shannon entropies for all the related states. Next, we obtained the position of the given avoided crossing by calculating the Shannon entropies intersection field strength for the two involved states. The Shannon entropies are calculated by using the one-electron wave functions derived from a well-established diagonalization method which is based on B-spline expansion technique and a parametric one-electron model potential. We have used this method to calculate a number of positions of both s and p states of avoided crossings for Rydberg potassium. The results are in excellent agreement with observed and other calculated results by using the ionization energies. Our study proves that Shannon entropy is an efficient information-theoretic parameter for characterization and prediction of avoided crossings of Rydberg potassium in the l-mixing region

A possible mechanism of <i>CTL1</i> in regulation of vesicle trafficking.

<p>(A, B) The seedlings of Col-0 and <i>sic1</i> grown on 1/2 MS medium (A) and 1/2 MS medium supplemented with 0.4% 1-butanol (B) for five days. The white dashed lines represent the root tip position when seedlings were transplanted. (C) The statistics analysis of the root growth of Col-0 and <i>sic1</i> on 1/2 MS with or without 1-butanol treatment. Data represent means ± SE, <i>n</i> = 6–7 for each genotype. Asterisks above the bar represent a statistically significant difference (<i>p</i> < 0.01) calculated using Student <i>t</i> test. (D) A hypothesized model of the mechanism of CTL1 involved in vesicle trafficking. The raw data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002978#pbio.2002978.s020" target="_blank">S1 Data</a>. Col-0, Columbia-0; CTL1, choline transporter-like 1; MS, Murashige and Skoog; PC, phosphatidylcholine; PLD phospholipase D; PM, plasma membrane; <i>sic1</i>, <i>significant ionome changes 1</i>; WT, wild-type.</p

CTL1 mediates endocytosis and secretory trafficking of PM proteins.

<p>(A) Internalization of FM4-64 in Col-0 and <i>sic1</i>. Images were taken at 10 minutes, 30 minutes, and 60 minutes after FM4-64 staining. The scale bars represent 10 μm. (B) The intracellular signal of FM4-64 in the root cells of Col-0 and <i>sic1</i> after FM4-64 staining. The data represent the means ± SD (<i>n</i> = 9). The images used in this analysis were captured using the same laser intensity. (C) Recycling of NRAMP1-GFP in the root epidermal cells of Col-0 and <i>sic1</i>. The seedlings were treated with 50 μM BFA for 1.5 hours (left panel) and then washed in water for 2 hours (right panel). (D) Statistical analysis of the percentages of root epidermal cells with BFA bodies after 2 hours of washing. The data represent the means ± SD. The asterisks above the bar represent a statistically significant difference (<i>p</i> < 0.01) calculated using Student <i>t</i> test, <i>n</i> = 3. (E) Recycling of NRAMP1-GFP in the root epidermal cells of Col-0 and <i>sic1</i> after CHX and BFA treatment. The seedlings were pretreated with 50 μM CHX for 30 minutes and then treated with 50 μM CHX and 50 μM BFA for 1.5 hours and then washed in water for 2 hours. The scale bars represent 10 μm. (F) Statistical analysis of the percentage of root epidermal cells with BFA bodies. The data represent the means ± SD. The asterisks above the bar represent a statistically significant difference (<i>p</i> < 0.01) calculated using Student <i>t</i> test, <i>n</i> = 3. (G) The structure of Golgi apparatus in the root cell of Col-0 and <i>sic1</i>. The arrows show the secretory vesicles close to Golgi apparatus. Scale bars represent 200 nm. (H) Quantification of secretory vesicles around Golgi apparatus. The data represent means ± SE. The asterisks above the bar represent a statistically significant difference (<i>p</i> < 0.01) calculated using Student <i>t</i> test, <i>n</i> = 18. The numerical data can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002978#pbio.2002978.s020" target="_blank">S1 Data</a>. BFA, brefeldin A; CHX, cycloheximide; Col-0, Columbia-0; CTL1, choline transporter-like 1; FM4-64, N-(3-Triethylammoniumpropyl)-4-(6-(4-(diethylamino)phenyl)hexatrienyl)pyridinium dibromide; GFP, green fluorescent protein; NRAMP1, natural resistance-associated macrophage protein 1; PM, plasma membrane; <i>sic1</i>, significant ionome changes 1.</p

Map-based cloning and complementation of <i>sic1</i>.

<p>(A) Mapping of <i>sic1</i> using 2030 F2 plants narrowed the location of the candidate gene down to a 100-kb region between the markers GM510 and GM524. The numbers under the markers are the number of recombinants between the indicated marker and <i>sic1</i>. (B) The gene structure of <i>CTL1</i> and the polymorphisms in <i>sic1</i> and <i>cher1-4</i>. (C) PCA of the leaf ionome of 5-week-old Col-0, <i>sic1</i>, and <i>cher1-4</i> and the F1 generation of <i>sic1</i> × <i>cher1-4</i> plants grown in artificial soil. PCA was based on the leaf concentrations of Na, Mn, Fe, Zn, and Mo (<i>n</i> = 12). (D-E) PCA of the leaf (D) and root (E) ionomes of 5-week-old Col-0 and <i>sic1</i>, as well as three independent transgenic complementation lines. PCA was based on the concentrations of Na, Mn, Fe, Zn, and Mo. <i>sic1</i>_CO1, <i>sic1</i> _CO2, and <i>sic1</i> _CO3 are three independent transgenic lines of <i>sic1</i> that were established with wild-type <i>pSIC1</i>::<i>SIC1-GFP</i> (<i>n</i> = 7). All raw data used for creating this figure can be accessed at <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002978#pbio.2002978.s020" target="_blank">S1 Data</a>. CTL1, choline transporter-like 1; Col-0, Columbia-0; Cys, cysteine; Fe, iron; Glu, glutamic acid; Gly, glycine; GM, genomic marker; Ile, isoleucine; Leu, leucine; Mn, manganese; Mo, molybdenum; PCA, principle component analysis; <i>sic1</i>, significant ionome changes 1; Val, valine; Zn, zinc.</p