The arabidopsis RCC1 family protein TCF1 regulates freezing tolerance and cold acclimation through modulating lignin biosynthesis

Cell water permeability and cell wall properties are critical to survival of plant cells during freezing, however the underlying molecular mechanisms remain elusive. Here, we report that a specifically cold-induced nuclear protein, Tolerant to Chilling and Freezing 1 (TCF1), interacts with histones H3 and H4 and associates with chromatin containing a target gene, BLUE-COPPER-BINDING PROTEIN (BCB), encoding a glycosylphosphatidylinositol-anchored protein that regulates lignin biosynthesis. Loss of TCF1 function leads to reduced BCB transcription through affecting H3K4me2 and H3K27me3 levels within the BCB gene, resulting in reduced lignin content and enhanced freezing tolerance. Furthermore, plants with knocked-down BCB expression (amiRNA-BCB) under cold acclimation had reduced lignin accumulation and increased freezing tolerance. The pal1pal2 double mutant (lignin content reduced by 30% compared with WT) also showed the freezing tolerant phenotype, and TCF1 and BCB act upstream of PALs to regulate lignin content. In addition, TCF1 acts independently of the CBF (C-repeat binding factor) pathway. Our findings delineate a novel molecular pathway linking the TCF1-mediated cold-specific transcriptional program to lignin biosynthesis, thus achieving cell wall remodeling with increased freezing tolerance

Preparation, characterization and photocatalytic activity of silicon and sulfur codoped mesoporous titanium dioxide photocatalyst

A series of mesoporous titanium dioxide (MTiO2) photocatalysts codoped with silicon and sulfur has been prepared by a template method using tetraethyl orthosilicate, thiourea and tetrabutyl titanate (Ti(OC4H9)4) as precursors and Pluronic P123 as template. The photoabsorbance of the prepared photocatalysts has been measured by UV-vis diffusive reflectance spectroscopy and its microstructure characterized using scanning electron microscopy, diffraction (XRD) and N2 adsorption-desorption measurements. The microcrystal of the codoped photocatalyst consistest of anatase phase and is present in the form of almost spherical particle. The photocatalytic activity has been studied by photodegradation of methyl blue in aqueous solution under UV and visible light irradiation. The results show that the amount of dopants, silicon and sulfur, influence the photoactivity. The photocatalyst codoped with 1 mol% silicon and 2 mol% sulfur exhibites the highest photoactivity. The synergistic effect of silicon and sulfur codoping in improves the photocatalytic activity considerably

Delving into Commit-Issue Correlation to Enhance Commit Message Generation Models

Commit message generation (CMG) is a challenging task in automated software engineering that aims to generate natural language descriptions of code changes for commits. Previous methods all start from the modified code snippets, outputting commit messages through template-based, retrieval-based, or learning-based models. While these methods can summarize what is modified from the perspective of code, they struggle to provide reasons for the commit. The correlation between commits and issues that could be a critical factor for generating rational commit messages is still unexplored. In this work, we delve into the correlation between commits and issues from the perspective of dataset and methodology. We construct the first dataset anchored on combining correlated commits and issues. The dataset consists of an unlabeled commit-issue parallel part and a labeled part in which each example is provided with human-annotated rational information in the issue. Furthermore, we propose \tool (\underline{Ex}traction, \underline{Gro}unding, \underline{Fi}ne-tuning), a novel paradigm that can introduce the correlation between commits and issues into the training phase of models. To evaluate whether it is effective, we perform comprehensive experiments with various state-of-the-art CMG models. The results show that compared with the original models, the performance of \tool-enhanced models is significantly improved.Comment: ASE2023 accepted pape

Mechanistic examination of causes for narrow distribution in an endangered shrub: a comparison of its responses to drought stress with a widespread congeneric species

Although deep rooting is usually considered a drought-tolerant trait, we found that Syringapinnatifolia, a deep rooting and hydrotropic shrub, has a limited distribution in arid areas. To elucidate the mechanisms for its narrow distribution, we conducted two experiments to examine the physiological and morphological responses to water availability and heterogeneity in S. pinnatifolia and a widespread congeneric species, S. oblata. We measured gas exchange, water use efficiency, and plasticity index in plants of these two species grown at different levels of soil water regimes and in containers with patched water distribution. Our results showed that high photosynthetic capacity in the narrowly distributed S. pinnatifolia was an important factor enabling its survival in the harsh sub-alpine environment. High photosynthetic capacity in S. pinnatifolia, however, was obtained at the expense of high transpiratory water loss, resulting in lower integrative water use efficiency. Biomass allocation to roots in S. pinnatifolia increased by 73 % when soil water increased from 75 to 95 % field capacity, suggesting that S. pinnatifolia could be less competitive for above-ground resources under favorable water regimes. The horizontal root hydrotropism and vertical root hydrotropism of S. pinnatifolia in soil with patched water patterns were likely related to compensation for leaf water loss at low soil water level, indicating a limited capacity for homeostasis within the plant for water conservation and lower level of inherent drought-tolerance. In summary, greater degree of morphological plasticity but lower degree of physiological adjustment may be the main causes for the hydrotropism and narrow distribution of S. pinnatifolia in the sub-alpine habitats

Attenuated Glial Reactivity on Topographically Functionalized Poly(3,4-Ethylenedioxythiophene):P-Toluene Sulfonate (PEDOT:PTS) Neuroelectrodes Fabricated by Microimprint Lithography

Following implantation, neuroelectrode functionality is susceptible to deterioration via reactive host cell response and glial scar-induced encapsulation. Within the neuroengineering community, there is a consensus that the induction of selective adhesion and regulated cellular interaction at the tissue–electrode interface can significantly enhance device interfacing and functionality in vivo. In particular, topographical modification holds promise for the development of functionalized neural interfaces to mediate initial cell adhesion and the subsequent evolution of gliosis, minimizing the onset of a proinflammatory glial phenotype, to provide long-term stability. Herein, a low-temperature microimprint-lithography technique for the development of micro-topographically functionalized neuroelectrode interfaces in electrodeposited poly(3,4-ethylenedioxythiophene):p-toluene sulfonate (PEDOT:PTS) is described and assessed in vitro. Platinum (Pt) microelectrodes are subjected to electrodeposition of a PEDOT:PTS microcoating, which is subsequently topographically functionalized with an ordered array of micropits, inducing a significant reduction in electrode electrical impedance and an increase in charge storage capacity. Furthermore, topographically functionalized electrodes reduce the adhesion of reactive astrocytes in vitro, evident from morphological changes in cell area, focal adhesion formation, and the synthesis of proinflammatory cytokines and chemokine factors. This study contributes to the understanding of gliosis in complex primary mixed cell cultures, and describes the role of micro-topographically modified neural interfaces in the development of stable microelectrode interfaces

Comparative genetic architectures of schizophrenia in East Asian and European populations

Schizophrenia is a debilitating psychiatric disorder with approximately 1% lifetime risk globally. Large-scale schizophrenia genetic studies have reported primarily on European ancestry samples, potentially missing important biological insights. Here, we report the largest study to date of East Asian participants (22,778 schizophrenia cases and 35,362 controls), identifying 21 genome-wide-significant associations in 19 genetic loci. Common genetic variants that confer risk for schizophrenia have highly similar effects between East Asian and European ancestries (genetic correlation = 0.98 ± 0.03), indicating that the genetic basis of schizophrenia and its biology are broadly shared across populations. A fixed-effect meta-analysis including individuals from East Asian and European ancestries identified 208 significant associations in 176 genetic loci (53 novel). Trans-ancestry fine-mapping reduced the sets of candidate causal variants in 44 loci. Polygenic risk scores had reduced performance when transferred across ancestries, highlighting the importance of including sufficient samples of major ancestral groups to ensure their generalizability across populations

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Schizophrenia has a heritability of 60-80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies

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