SoyTEdb: a comprehensive database of transposable elements in the soybean genome

<p>Abstract</p> <p>Background</p> <p>Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop.</p> <p>Description</p> <p>Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study.</p> <p>Conclusion</p> <p>SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.</p

Methylprednisolone as Adjunct to Endovascular Thrombectomy for Large-Vessel Occlusion Stroke

Importance It is uncertain whether intravenous methylprednisolone improves outcomes for patients with acute ischemic stroke due to large-vessel occlusion (LVO) undergoing endovascular thrombectomy. Objective To assess the efficacy and adverse events of adjunctive intravenous low-dose methylprednisolone to endovascular thrombectomy for acute ischemic stroke secondary to LVO. Design, Setting, and Participants This investigator-initiated, randomized, double-blind, placebo-controlled trial was implemented at 82 hospitals in China, enrolling 1680 patients with stroke and proximal intracranial LVO presenting within 24 hours of time last known to be well. Recruitment took place between February 9, 2022, and June 30, 2023, with a final follow-up on September 30, 2023.InterventionsEligible patients were randomly assigned to intravenous methylprednisolone (n = 839) at 2 mg/kg/d or placebo (n = 841) for 3 days adjunctive to endovascular thrombectomy. Main Outcomes and Measures The primary efficacy outcome was disability level at 90 days as measured by the overall distribution of the modified Rankin Scale scores (range, 0 [no symptoms] to 6 [death]). The primary safety outcomes included mortality at 90 days and the incidence of symptomatic intracranial hemorrhage within 48 hours. Results Among 1680 patients randomized (median age, 69 years; 727 female [43.3%]), 1673 (99.6%) completed the trial. The median 90-day modified Rankin Scale score was 3 (IQR, 1-5) in the methylprednisolone group vs 3 (IQR, 1-6) in the placebo group (adjusted generalized odds ratio for a lower level of disability, 1.10 [95% CI, 0.96-1.25]; P = .17). In the methylprednisolone group, there was a lower mortality rate (23.2% vs 28.5%; adjusted risk ratio, 0.84 [95% CI, 0.71-0.98]; P = .03) and a lower rate of symptomatic intracranial hemorrhage (8.6% vs 11.7%; adjusted risk ratio, 0.74 [95% CI, 0.55-0.99]; P = .04) compared with placebo. Conclusions and Relevance Among patients with acute ischemic stroke due to LVO undergoing endovascular thrombectomy, adjunctive methylprednisolone added to endovascular thrombectomy did not significantly improve the degree of overall disability.Trial RegistrationChiCTR.org.cn Identifier: ChiCTR210005172

AN ALTERNATIVE APPROACH TO INSTITUTIONAL ANALYSIS IN STRATEGIC ENVIRONMENTAL ASSESSMENT IN CHINA

This paper advocates a modification of the impact-based approach to strategic environmental assessment (SEA) which seems unable to address institutional weaknesses in most conventional SEA cases in China. It identifies a possible alternative approach, i.e. an impact-centred SEA with institutional components, and presents an analytical framework for institutional analysis, including a four-phase methodology to address and improve institutional weaknesses. Subsequently, the analytical framework is applied to an SEA pilot for a provincial transport plan in China. The case study demonstrates (1) that the proposed approach is adequate even in relatively fixed SEA processes; and (2) that the components and the logical relationships among factors elaborated on in the analytical framework are reasonable. In addition, the components of the framework that need to be improved and the perspectives for future application are discussed.Strategic environmental assessment, institutional analysis, provincial transport plan, environmental management, Hubei, China

Strength–ductility trade-off in TiB-TC4 composites with a pseudo core–shell structure

Heterogeneous structure is practical to improve the strain hardening abilities of materials due to the effect of hetero-deformation induced hardening, especially of composites. In this study, a series of TiB/TC4 composites with a pseudo core–shell structure of bimodal grain distribution were fabricated via a two-step ball-milling and spark plasma sintering. The synthesized TiB/TC4 composites have a structure of coarse lamella α-Ti grains of average 23.6 μm in diameter surrounded by fine α-Ti lamella grains of average 4.2 μm, with TiB distributed on the primary TC4 surface areas. TiB/TC4 composites with 0.4 wt% TiB2 exhibited the best comprehensive mechanical properties with an ultimate tensile strength of 1161.95 MPa (a 35.1% increase compared with that of pure TC4) and an elongation of 7.57%. In conclusion, the pseudo core–shell structure improved the strength by improving the strain-hardening abilities, achieved by the coordinated deformation between coarse grains and fine grains

Chrysanthemum dabieshanense, a new name for Chrysanthemum vestitum var. latifolium (Asteraceae, Anthemideae)

Recent phylogenetic analyses have revealed that Chrysanthemum vestitum var. latifolium and C. vestitum var. vestitum were placed in different clades based on their chloroplast genomes and nuclear LFAFY gene sequences. Accordingly, based on previous morphological analysis, molecular phylogenetic results, fieldwork, and herbarium studies, Chrysanthemum vestitum var. latifolium should be raised to the species level. Considering the condition of the material found and Articles 6.9, 6.11, 41.2, 58.1 of the International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code) that is currently in force, Chrysanthemum dabieshanense Z.X.Fu, A.G.Zhen, & Y.P.Ma, nom. nov. is proposed as the new name for Chrysanthemum vestitum var. latifolium J.Zhou & Jun Y.Chen. The detailed emended description, distribution map, insights into its habitat, and an updated comparative morphological study are presented in this study

Influence of Height–Diameter Ratio on Rock Compressive Failure Characteristics and Damage Evolution Law

In underground projects such as mining and tunneling, the presence of coal rock columns plays a certain supporting role, and the instability of coal rock columns is often related to their size and shape of presence. Therefore, in order to investigate the compressive damage characteristics and damage evolution law of rocks of different sizes, uniaxial compression tests were conducted on sandstones with different height−diameter ratios to explore the mechanical properties and damage characteristics of sandstones with different height−diameter ratios, analyze the connection between acoustic emission ringing count rate, accumulated energy, peak frequency, and b-value changes and height–diameter ratio, and analyze the evolution law of sandstones during damage based on damage variables, and draw the following conclusions. As the height-to-diameter ratio increases, the less affected by the end effect, the rock strength shows a nonlinear decreasing trend, and the decreasing trend becomes slow. The acoustic emission ringing count rate evolved from intermittent to continuous occurrence, showing multiple peaks as the test proceeded. The accumulated energy rises sharply before rupturing after several steps from stable development. As the height-to-diameter ratio increases, the acoustic emission signal before rupture rises more intensively, and the damage is more concentrated. The overall level of the b-value shows an increasing trend, the proportion of acoustic emission high-frequency signal gradually increases, and the development of tiny cracks inside the rock more intensively. Therefore, the sudden change of acoustic emission signal can be used as a precursor of rock damage. The rock damage curve has smaller values in the stable damage phase. With the increase in the height-to-diameter ratio, the non-stable damage stage damage showed a trend of decreasing and then increasing and reached the minimum at L/D = 2.0

Influence of Height&ndash;Diameter Ratio on Rock Compressive Failure Characteristics and Damage Evolution Law

In underground projects such as mining and tunneling, the presence of coal rock columns plays a certain supporting role, and the instability of coal rock columns is often related to their size and shape of presence. Therefore, in order to investigate the compressive damage characteristics and damage evolution law of rocks of different sizes, uniaxial compression tests were conducted on sandstones with different height&minus;diameter ratios to explore the mechanical properties and damage characteristics of sandstones with different height&minus;diameter ratios, analyze the connection between acoustic emission ringing count rate, accumulated energy, peak frequency, and b-value changes and height&ndash;diameter ratio, and analyze the evolution law of sandstones during damage based on damage variables, and draw the following conclusions. As the height-to-diameter ratio increases, the less affected by the end effect, the rock strength shows a nonlinear decreasing trend, and the decreasing trend becomes slow. The acoustic emission ringing count rate evolved from intermittent to continuous occurrence, showing multiple peaks as the test proceeded. The accumulated energy rises sharply before rupturing after several steps from stable development. As the height-to-diameter ratio increases, the acoustic emission signal before rupture rises more intensively, and the damage is more concentrated. The overall level of the b-value shows an increasing trend, the proportion of acoustic emission high-frequency signal gradually increases, and the development of tiny cracks inside the rock more intensively. Therefore, the sudden change of acoustic emission signal can be used as a precursor of rock damage. The rock damage curve has smaller values in the stable damage phase. With the increase in the height-to-diameter ratio, the non-stable damage stage damage showed a trend of decreasing and then increasing and reached the minimum at L/D = 2.0

The complete chloroplast genome of Impatiens uliginosa Franch., an endemic species in Southwest China

The complete chloroplast genome sequence of Impatiens uliginosa Franch., an endemic species in Southwest China, we research genetic and phylogenetic relationship with other species in an effort to provide genomic resources useful for promoting its conservation and utilization. The total chloroplast genome size of I. uliginosa is 152,609 bp, with a typical quadripartite structure including a pair of inverted repeat (IRs, 25,871 bp) regions separated by a small single copy (SSC, 17,502 bp) region and a large single copy (LSC, 83,365 bp) region. The overall GC content of I. uliginosa plastid genome was 36.8%. The whole chloroplast genome contains 136 genes, including 89 protein-coding genes (PCGs), 38 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes (rRNAs). Among these genes, 15 genes have one intron and 2 genes contain two introns. To investigate the evolution status, the phylogenetic tree based on APG III from 12 complete chloroplast plastomes of Ericales supports close relationships. According to the phylogenetic topologies, I. uliginosa was closely related to I. piufanensis