Insights into salt tolerance from the genome of Thellungiella salsuginea

Thellungiella salsuginea, a close relative of Arabidopsis, represents an extremophile model for abiotic stress tolerance studies. We present the draft sequence of the T. salsuginea genome, assembled based on ∼134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. This genome provides resources and evidence about the nature of defense mechanisms constituting the genetic basis underlying plant abiotic stress tolerance. Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

A Fatigue Crack Size Evaluation Method Based on Lamb Wave Simulation and Limited Experimental Data

This paper presents a systematic and general method for Lamb wave-based crack size quantification using finite element simulations and Bayesian updating. The method consists of construction of a baseline quantification model using finite element simulation data and Bayesian updating with limited Lamb wave data from target structure. The baseline model correlates two proposed damage sensitive features, namely the normalized amplitude and phase change, with the crack length through a response surface model. The two damage sensitive features are extracted from the first received S0 mode wave package. The model parameters of the baseline model are estimated using finite element simulation data. To account for uncertainties from numerical modeling, geometry, material and manufacturing between the baseline model and the target model, Bayesian method is employed to update the baseline model with a few measurements acquired from the actual target structure. A rigorous validation is made using in-situ fatigue testing and Lamb wave data from coupon specimens and realistic lap-joint components. The effectiveness and accuracy of the proposed method is demonstrated under different loading and damage conditions

The effects of different shapes of capsulorrhexis on postoperative refractive outcomes and the effective position of the intraocular lens in cataract surgery

Abstract Background To evaluate the effects of anterior capsular opening size on deviation from predicted refraction and the effective position of the intraocular lens (ELP) in cataract surgery. Methods Nonrandomized clinical trial. Eighty patients (80 eyes) with simple age-related cataracts were treated from May 2018 to September 2018 at the Fourth Affiliated Hospital of China Medical University. All patients undergoing phacoemulsification received intraocular lens based on the voluntary principle. Forty eyes were implanted with the C-loop haptic intraocular lens (AMO Tecnis ZCB00) while the other 40 eyes were implanted with the plate haptic intraocular lens (CT ASPHINA 509 M). Follow-up visits were conducted postoperatively at 1 week, 1 month, and 3 months during which patients underwent refraction and data collection after pupil dilation, which included anterior segment photography and Scheimpflug imaging by Pentacam. The area, horizontal and vertical diameter of the capsulorrhexis, circularity, decentration, and package were analysed using the image analysis software Image-Pro-Plus 6.0,then evaluated the relationship between the different shapes of capsulorrhexis with deviation from predicted refraction and ELP in cataract surgery. Results Deviation from predicted refraction and all of the parameters of capsulorrhexis were not correlative in the 509 M IOL group, however, in the Tecnis IOL group, while the deviation from predicted refraction and all of the capsulorrhexis parameters were not correlative at 1 week, the deviation from predicted refraction did correlate with capsulorrhexis area, horizontal diameter at 1 month (P = 0.029, P = 0.048), and with capsulorrhexis area, vertical diameter at 3 months (P = 0.03, P = 0.017). The ELP correlated with package in both groups postoperatively (r > 0, P  0.05). For the Tecnis IOL group, the ELP and capsulorrhexis area were correlated at 1 week and 1 month, while the ELP and horizontal diameter, the ELP and vertical diameter were correlated at 1 week, but did not correlate with the other capsulorrhexis parameters in the Tecnis IOL group (all P > 0.05). Conclusions The shape of the capsulorrhexis has an effect on postoperative refractive outcomes and the effective position of the intraocular lens in cataract surgery, and plate haptic intraocular lenses have better refractive stability than C-loop haptic intraocular lenses. Trial registration ChiCTR1800015638,2018-04-12

A Novel Safety Assessment Framework for Pavement Friction Evolution Due to Traffic on Horizontal Curves

The friction coefficient is one of the dominant parameters affecting vehicle driving stability on horizontal curves. However, there is no comprehensive framework to assess the traffic safety on the horizontal curve with the evolution of the friction coefficient caused by the traffic flow. In light of this, this paper developed an integrated risk-assessment framework to evaluate the safety on the horizontal curve with the friction coefficient evolving under different traffic characteristics. The speed distribution on the horizontal curve of the freeway is obtained through field experiments that serve as the basic parameters of the model. A new multi-vehicle risk index (MRI) is introduced to assess the traffic safety risk for the horizontal curve by coupling the reliability theory and negative binomial. Three traffic characteristics are considered in the analysis: cumulative traffic volume (CTV), annual average daily traffic (AADT), and average daily traffic of heavy goods vehicles (AADTHGV). The results show that the AADT and AADTHGV have a considerable impact on the road risk level. When the truck traffic volume is less than 1000 veh/d, the risk of horizontal curves changes less as road operational time goes. The research results can provide a reference for the road maintenance department to determine the timing of road maintenance

Triarylborane‐Functionalized Au8Ag8(CCR)16 Nanocluster with Enhanced Lewis Acidity

Abstract Functionalization of ligated metal nanoclusters with versatile ligands is highly desired for wide applications. Lewis acids have shown promise in multiple realms such as self‐assembly and catalysis, which may endow nanoclusters with diverse functions. However, metal nanoclusters with Lewis acid surface have not been reported. Here, the functionalization of a bimetallic nanocluster Au8Ag8(CCR)16 with triarylborane (TAB) is reported, which exhibits enhanced Lewis acidity. By using single‐crystal X‐ray crystallography, the structure of the nanocluster with 16 boron receptor sites is confirmed, which presents ≈15‐fold enhancement of quenching efficiency in sensing fluoride compared to that of free triarylborane ligand. By the combined analysis using ultrafast transient absorption and photoluminescent (PL) decay measurements, the quenching mechanism of Au8Ag8 to fluoride is elucidated. The PL quenching is realized via two pathways with enhanced non‐radiation energy dissipation, i.e., prolonged electron–phonon coupling and reverse intersystem crossing (RISC). This work may open a new route to diverse applications of metal nanoclusters

In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation

Abstract Background Harnessing hepatocytes for basic research and regenerative medicine demands a complete understanding of the genetic determinants underlying hepatocyte differentiation and maturation. Single-cell CRISPR screens in organoids could link genetic perturbations with parallel transcriptomic readout in single cells, providing a powerful method to delineate roles of cell fate regulators. However, a big challenge for identifying key regulators during data analysis is the low expression levels of transcription factors (TFs), which are difficult to accurately estimate due to noise and dropouts in single-cell sequencing. Also, it is often the changes in TF activities in the transcriptional cascade rather than the expression levels of TFs that are relevant to the cell fate transition. Results Here, we develop Organoid-based Single-cell CRISPR screening Analyzed with Regulons (OSCAR), a framework using regulon activities as readouts to dissect gene knockout effects in organoids. In adult-stem-cell-derived liver organoids, we map transcriptomes in 80,576 cells upon 246 perturbations associated with transcriptional regulation of hepatocyte formation. Using OSCAR, we identify known and novel positive and negative regulators, among which Fos and Ubr5 are the top-ranked ones. Further single-gene loss-of-function assays demonstrate that Fos depletion in mouse and human liver organoids promote hepatocyte differentiation by specific upregulation of liver metabolic genes and pathways, and conditional knockout of Ubr5 in mouse liver delays hepatocyte maturation. Conclusions Altogether, we provide a framework to explore lineage specifiers in a rapid and systematic manner, and identify hepatocyte determinators with potential clinical applications

Hyaluronic Acid-Templated Ag Nanoparticles/Graphene Oxide Composites for Synergistic Therapy of Bacteria Infection

Developing methods of decreasing the harm to cell and increasing the antibacterial efficiency is becoming a potential topic of medical treatments. We demonstrated a hyaluronidase-triggered photothermal platform for killing bacteria based on silver nanoparticles (AgNPs) and graphene oxide (GO). The property of the hyaluronidase (HAase)-triggered release provided excellent antibacterial activity against <i>Staphylococcus aureus</i>. Upon illumination of NIR light, the GO-based nanomaterials locally raised the temperature, resulting in high mortality of bacteria. The HAase-triggered AgNPs releasing approach for antibacterial allows AgNPs to be protected by hyaluronic acid (HA) template without affecting mammalian cells. The nanocomposites provided antibacterial activity against <i>S. aureus</i> while showing low toxicity to mammal cells. In addition, the GO–HA–AgNPs are prepared for in vivo experiments and show excellent antibacterial property in wound disinfection model

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/ GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5(DEL1+ IN1), and GSE5(DEL2)) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5 DEL1+ IN1 haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5 DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice