Chemokine-like factor 1 (CKLF1) is expressed in myocardial ischemia injury in vivo and in vitro

Introduction:Chemokine-like factor 1(CKLF1)is a chemokine that is overexpressed in several diseases.Our previousfindings revealed a significant increase in CKLF1 expression in the ischemic brain,suggesting its potential as a therapeutic target for ischemic stroke.Methods:In this study,we examined the expression dynamics of CKLF1 in both in vivo and in vitro models of ischemic cardiac injury.Myocardial infarction(MI)was induced in vivo by ligation of the left anterior descending artery(LAD)of the rat heart.The levels of CKLF1,Creatine Kinase MB Isoenzyme(CK-MB),and Lactate dehydrogenase(LDH)in the serum were detected using Enzyme-linked immunosorbent assay(ELISA).The expression of CKLF1 in the infarcted area was detected by immunohistochemistry,immunofluorescence,quantitative PCR(qPCR),and Western blotting(WB).H9C2 and AC16 cardiomyocytes cultured in vitro were subjected to oxygen and glucose deprivation(OGD).LDH was used to detect cell damage,and CKLF1 expression was detected by qPCR and WB.Results:CKLF1 mRNA and protein expression were significantly increased in h9c2 cells at 1.5 h and in AC16 cells at 4 h after OGD.The serum CK-MB in rats increased significantly on thefirst day after infarction,while the LDH concentration increased significantly on the third day after infarction.CKLF1 blood levels significantly increased on thefirst day following MI in rats.CKLF1 expression notably increased in the infarct area on days 1,3,and 7 post-MI.In MI tissue,CKLF1 colocalizes with cardiomyocytes,macrophages,and neutrophils.Conclusion:CKLF1 was substantially expressed during myocardial ischemia injury both in vivo and in vitro and was colocalized with macrophages and neutrophils,indicating that CKLF1 is expected to be a biomarker and a drug target for the treatment of myocardial infarction.

Light-stabilized GIL1 suppresses PIN3 activity to inhibit hypocotyl gravitropism

Light and gravity coordinately regulate the directional growth of plants.Arabidopsis Gravitropic in the Light 1(GIL1)inhibits the negative gravitropism of hypocotyls in red and far-red light,but the underlying molecular mechanisms remain elusive.Our study found that GIL1 is a plasma membrane-localized protein.In endodermal cells of the upper part of hypocotyls,GIL1 controls the negative gravitropism of hypocotyls.GIL1 directly interacts with PIN3 and inhibits the auxin transport activity of PIN3.Mutation of PIN3 suppresses the abnormal gravitropic response of gil1 mutant.The GIL1 protein is unstable in darkness but it is stabilized by red and far-red light.Together,our data suggest that light-stabilized GIL1 inhibits the negative gravitropism of hypocotyls by suppressing the activity of the auxin transporter PIN3,thereby enhancing the emergence of young seedlings from the soil.

CRISPR-detector:fast and accurate detection,visualization,and annotation of genome-wide mutations induced by genome editing events

The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing.To track on/off-target events with emerging new editing techniques,improved bioinformatic tools are indispensable.Existing tools suffer from limitations in speed and scalability,especially with whole-genome sequencing(WGS)data analysis.To address these limitations,we have developed a comprehensive tool called CRISPR-detector,a web-based and locally deployable pipeline for genome editing sequence analysis.The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline,with additional novel annotation and visualization modules designed to fit CRISPR applications.Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing.CRISPR-detector offers optimized scalability,enabling WGS data analysis beyond Browser Extensible Data file-defined regions,with improved accuracy due to haplotype-based variant calling to handle sequencing errors.In addition,the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users.These advantages facilitate rapid and efficient detection of mutations induced by genome editing events,especially for datasets generated from WGS.The web-based version of CRISPR-detector is available at https://db.cngb.org/crispr-detector,and the locally deployable version is available at https://github.com/hlcas/CRISPR-detector.

Corrigendum to“CRISPR-detector:fast and accurate detection,visualization,and annotation of genome-wide mutations induced by genome editing events”[Journal of Genetics and Genomics(2023)563-572]

This corrigendum clarifies information in the article“CRISPR-detector:fast and accurate detection,visualization,and annotation of genomewide mutations induced by genome editing events”by Huang et al.(2023).In the figure legend of Fig.S1,the sentence“CRISPR-detector failed to report insertions larger than 72 bp while CRISPResso2 failed to report insertions larger than 53 bp.”should be corrected into“CRISPR-detector failed to report deletions larger than 71 bp while CRISPResso2 failed to report deletions larger than 53 bp.”

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

A high-density single nucleotide polymorphism （SNP） array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the devel- opment of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for dif- ferent objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies （GWAS） analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization

Light serves as the source of energy as well as an information signal for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signaling are still lacking. In this study, we took advantage of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domain to identify orthologous genes of core components involved in light perception and signaling and to reconstruct their evolutionary history. Our analyses suggested that acclimation to different distribution of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water and enabled plants to deal with ultraviolet B light (UV-B). After acquisition of UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize water surface where red light became the prominent light energy source. The seedling emergence pathway, which is mediated by a combination of light and phytohormone signals that orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of the plant and animal kingdoms, the coevolution and optimization of light perception and downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.

Arabidopsis DET1 Represses Photomorphogenesis in Part by Negatively Regulating DELLA Protein Abundance in Darkness

Arabidopsis De-etiolated 1 （DET1） is one of the key repressors that maintain the etiolated state of seedlings in darkness. The plant hormone gibberellic acid （GA） also participates in this process, and plants deficient in GA synthesis or signaling show a partially de.etiolated phenotype in darkness. However, how DET1 and the GA pathway work in concert in repressing photomorphogenesis remains largely unknown. In this study, we found that the abundance of DELLA proteins in detl-1 was increased in comparison with that in the wildtype plants. Mutation in DET1 changed the sensitivity of hypocotyl elongation of mutant seedlings to GA and paclobutrazol （PAC）, an inhibitor of GA synthesis. However, we did not find obvious differences between detl-1 and wild-type plants with regard to the bioactive GA content or the GA signaling upstream of DELLAs. Genetic data showed that removal of several DELLA proteins suppressed the detl-1 mutant phenotype more obviously than GA treatment, indicating that DET1 can regulate DELLA proteins via some other mechanisms. In addition, a large-scale transcriptomic analysis revealed that DET1 and DELLAs play antagonistic roles in regulating expression of photosynthetic and cell elongation-related genes in etiolated seedlings. Taken together, our results show that DET1 represses photomorphogenesis in darkness in part by reducing the abundance of DELLA proteins.

Application of Optical Tweezers in the Research of Molecular Interaction between Lymphocyte Function Associated Antigen-1 and Its Monoclonal Antibody

Lymphocyte function associated antigen-1 （CD11a/CD18, LFA-1） plays an important role in the structure of the immunological synapse and is required for efficient lysis of cytotoxic T lymphocytes （CTLs） and natural killer （NK） cells. To study the activation mode of LFA-1 on the NK cell surface, optical tweezers were used in the work. As an emerging technology, optical tweezers are widely used to manipulate microscopic objects and measure the forces of molecular interactions in the field of biological research. In our study, a new platform was constructed to study the single molecular behavior of receptor on cell surface using optical tweezers. Based on the platform, the interaction between an NK cell and a polystyrene microsphere coated with anti-LFA-1 antibody was observed. The result confirmed that the adhesion forces between an NK cell and a polystyrene bead were time-dependent. According to our findings, we propose that anti-LFA-1 antibody may cause the clustering of LFA-1 on NK cell surface. Cellular ＆ Molecular Immunology.

A novel CRISPR/Cas9 system for efficiently generating Cas9- free multiplex mutants in Arabidopsis

The CRISPR/Cas9 genome-editing system has emerged as a popular powerful tool for biological research.However,the process of selecting efficiently edited Cas9-free plants is usually laborious and time consuming.Here,we demonstrated P2A to be the most efficient self-cleaving peptide for fusing Cas9 and GFP in Arabidopsis and then used Cas9-P2A-GFP to develop a novel CRISPR/Cas9 system.Additionally,a pair of isocaudomer restriction enzymes were selected to conveniently assemble multiple sgRNAs.In this system,the GFP fluorescence intensity in T1 transgenic plants indicates the expression level of the Cas9 protein,which correlates well with the editing efficiency.Furthermore,Cas9-free plants can be easily selected by examining GFP fluorescence in T2 transgenic plants.The efficient knockout of BRI1,BZR1 and BES1 demonstrated the robustness of our new system.Thus,we designed a novel CRISPR/Cas9 system that can generate Cas9-free multiplex mutants efficiently in Arabidopsis and possibly in other plant species.

FRET-based polymer materials for detection of cellular microenvironments

Effective detection of cellular microenvironments and understanding of physiological activities in living cells remain a considerable challenge.In recent years,fluore scence(or Forster)resonance energy trans fe r(FRET)technology has emerged as a valuable method for real-time imaging of intracellular environment with high sensitivity,specificity and spatial resolution.Particularly,polymer-based imaging systems show enhanced stability,improved biodistribution,increased dye payloads,and amplified signal/noise ratio compared with small molecular sensors.This review summarizes the recent progress in FRET-based polymeric systems for probing the physiological environments in cells.

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the Golden Gate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus （QTL） mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines （RILs） derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorpbic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted mark- ers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quanti- tative trait loci （QTLs） with phenotypic variation explained （PVE） values〉5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterili- ty-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construc- tion and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of in- ter-subspecies hybrid sterility and correlations with important agronomic traits in rice.