Identification of QTL for kernel number-related traits in a rice chromosome segment substitution line and fine mapping of qSP1

A chromosome segment substitution line (CSSL) is a powerful tool for combining quantitative trait locus (QTL) mapping with the pyramiding of desirable alleles. The rice CSSL Z1364 with increased kernel number was identified in a BC3F8 population derived from a cross of Nipponbare as the recipient with Xihui 18 as the donor parent. Z1364 carried three substitution segments distributed on chromosomes 1, 6, and 8. The mean substitution length was 1.19 Mb. Of 17 QTL identified on the substitution segments, qSP1 for spikelets per panicle, qSSD1 for seed-set density, and qNSB1 for number of secondary branches explained respectively 57.34%, 87.7%, and 49.44% of the corresponding phenotypic variance and were all linked to RM6777. Chi-square analysis showed that the increased kernel number in Z1364 was inherited recessively by a single gene. By fine mapping, qSP1 was delimited to a 50-kb region on the short arm of chromosome 1. Based on DNA sequence, a previously uncharacterized rice homolog of Arabidopsis thaliana AT4G32551 was identified as a candidate gene for qSP1 in which mutation increases the number of spikelets and kernels in Z1364. qSP1 was expressed in all tissues, but particularly in 1-cm panicles. The expression levels of OsMADS22, GN1A, and DST were upregulated and those of LAX2, GNP1, and GHD7 were downregulated in Nipponbare. These results provide a foundation for functional research on qSP1.

Real-time analysis of inflammatory cytokines and regulatory gene expression in tissues surrounding the hematoma after intracerebral hemorrhage

BACKGROUND： Secondary lesions can occur in tissues surrounding the hematoma following intracerebral hemorrhage, with the presence of inflammatory reactions, cytokine expression and apoptosis These have been confirmed in animal studies. Our study sought to determine whether these could be detected in human tissues surrounding the hematoma following intracerebral hemorrhage. OBJECTIVE： To investigate expression of inflammatory cytokines, Bax and Bcl-x, and identify neural cell apoptosis in tissues surrounding the hematoma, and to analyze the correlation between them and pathological damage in intracerebral hemorrhage patients. DESIGN, TIME AND SETTING： This histopathology, controlled study was performed at the Department of Neurosurgery, Sichuan People＇s Hospital, China, from January 2003 to January 2005. PARTICIPANTS： Brain tissues 1 cm from the hematoma in 30 intracerebral hemorrhage patients served as the experimental group. Brain tissues located away from the hematoma in 7 patients served as the control group. METHODS： TUNEL was used to detect neural cell apoptosis. Immunohistochemistry （labeled dextran polymer） and RT-PCR were used to measure tumor necrosis factor- α, interleukin-1 β, interleukin-6, Bax and Bcl-x protein and mRNA expression. Pathological changes in brain tissues surrounding the hematoma were observed following HE staining. MAIN OUTCOME MEASURES： Neural cell apoptosis, inflammatory cytokines, Bax and Bcl-x protein and mRNA expression, pathological changes in brain tissues surrounding the hematoma. RESULTS： Brain tissues surrounding the hematoma were mildly damaged within 6 hours, severely damaged at 24-72 hours, and significantly improved 1 week following intracerebral hemorrhage. Expression of tumor necrosis factor- α protein and mRNA, interleukin-1β and interleukin-6 mRNA was not significant in tissues surrounding the hematoma, which was identical to the control group within 6 hours after intracerebral hemorrhage. This expression was significantly higher compared with the control group from 12-72 hours, and gradually decreased after 72 hours. The number of apoptotic neural cells reached a peak between 12- 72 hours. Tumor necrosis factor-α protein and mRNA, interleukin-1β and interleukin-6 mRNA levels were positively correlated with apoptosis, Bax protein and mRNA levels （P 〈 0.01 ）. CONCLUSION： Tumor necrosis factor-α, interleukin-1β, and interleukin-6 levels are highly correlated with apoptosis. With the decrease in tumor necrosis factor-α, interleukin-1β and interleukin-6 levels, the number of apoptotic cells gradually reduced.

Identification of LRRC46 as a novel candidate gene for high myopia

High myopia(HM)is the primary cause of blindness,with the microstructural organization and composition of collagenous fibers in the cornea and sclera playing a crucial role in the biomechanical behavior of these tissues.In a previously reported myopic linkage region,MYP5(17q21-22),a potential candidate gene,LRRC46(c.C235T,p.Q79X),was identified in a large Han Chinese pedigree.LRRC46 is expressed in various eye tissues in humans and mice,including the retina,cornea,and sclera.In subsequent cell experiments,the mutation(c.C235T)decreased the expression of LRRC46 protein in human corneal epithelial cells(HCE-T).Further investigation revealed that Lrrc46^(-/-)mice(KO)exhibited a classical myopia phenotype.The thickness of the cornea and sclera in KO mice became thinner and more pronounced with age,the activity of limbal stem cells decreased,and microstructural changes were observed in the fibroblasts of the sclera and cornea.We performed RNA-seq on scleral and corneal tissues of KO and normal control wild-type(WT)mice,which indicated a significant downregulation of the collagen synthesis-related pathway(extracellular matrix,ECM)in KO mice.Subsequent in vitro studies further indicated that LRRC46,a member of the important LRR protein family,primarily affected the formation of collagens.This study suggested that LRRC46 is a novel candidate gene for HM,influencing collagen protein VⅢ(Col8a1)formation in the eye and gradually altering the biomechanical structure of the cornea and sclera,thereby promoting the occurrence and development of HM.

Erratum to:CD146 as a promising therapeutic target for retinal and choroidal neovascularization diseases

Erratum to:Sci China Life Sciences,Volume 65,Issue 6:1157-1170(2022),https://doi.org/10.1007/s11427-021-2020-0This paper contains four errors in Figure 4 and Figure 5.In Figure 4C,the image labeled as"1%O_(2)+IgG ctrl"is incorect.This image is another one for 1%O_(2) group.We provide a new image as follows for 1%O_(2)+IgG ctrl group.This new image does not affect the conclusion of this article.

ERRATUM TO:Cholesterol homeostasis regulated by ABCA1 is critical for retinal ganglion cell survival

Erratum to:SCIENCE CHINA Life Sciences,Volume 66,Issue 2:211-225(2022),https://doi.org/10.1007/s11427-021-2126-2 This paper contains an error in Figure 4C,where the representative images of filipin staining of retinal sections from 6-month-old mice were misused.We provide the correct picture for Figure 4C as follows.The statistical result in Figure 4D was corrected as well.This new Figure 4 does not affect the conclusion of this article.

Association analysis of genetic variants in critical patients with COVID-19 and validation in a Chinese population

Dear Editor,Genome-wide association studies(GWASs)have reported a genetic association between certain populations and the severity of COVID-19.In severe patients,changes in the locus 3p21.31(including SLC6A20,LZTFL1,CCR9,FYCO1,CXCR6,and XCR1)are associated with COVID-19 hospitalization(Ellinghaus et al.,2020).Moreover,variations in 9p34.2 region(including genes related to the ABO blood grouping)can affect both susceptibility and severity of COVID-19;in particular,individuals with blood group A may have an increased risk of COVID-19 infection,while those with blood group O may have a protective effect(Ellinghaus et al.,2020;Shelton et al.,2021).

Morphological and physiological analysis of narrow and striped leaf 1(nsl1) mutant of rice(Oryza sativa L.) and the gene mapping

The shape and color of rice leaves are important agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality.A new mutant exhibiting stable inheritance was identified as derived from ethyl methane sulfonate(EMS)-treated restorer Jinhui 10,tentatively named as narrow and striped leaf 1(nsl1).The nsl1 displayed pale white leaves at the seeding stage and then white striped leaves in parallel to the main vein at the jointing stage.Meanwhile,its leaf blades are significantly narrower than the control group of Jinhui 10.The chloroplast structures of cells in the white striped area of the nsl1 mutant break down,and the photosynthetic pigments are significantly lower than that of the wild type.Moreover,fluorescence parameters,such as F0,F v/F m,U psII,qp,and ETR,in the nsl1 mutant are significantly lower than those of the wild type,and the photosynthetic efficiency is also significantly decreased.These changes in leaf color and shape,together with physiological changes in the nsl1,result in smaller plant height and a decrease in the most important agronomic traits,such as the number of grains per panicle,grain weight,etc.Genetic analysis shows that the narrow and striped traits of the nsl1 mutant are controlled by a single recessive nuclear gene,which is located between InDel 16and InDel 12 in chromosome 3.The physical distance is204 kb.So far,no similar genes of such leaf color and shape in this area have been reported.This study has laid a solid foundation for the gene cloning and function analysis of NSL1.

Detection of serum IgM and IgG for COVID-19 diagnosis

Dear Editor,Infection with the novel coronavirus(SARS-CoV-2,which is the virus responsible for the coronavirus disease 2019(COVID-19))was first reported in Wuhan,China on December 31,2019.The outbreak of COVID-19 remains ongoing and was linked to more than 80,000 infected patients and more than 3,000 deaths in China as of March 7,2020(Holshue et al.,2020).

Irregular distribution of wind power prediction

Wind power is volatile and uncertain, which makes it difficult to establish an accurate prediction model.How to quantitatively describe the distribution of wind power output is the focus of this paper. First, it is assumed that wind speed is a random variable that satisfies the normal distribution. Secondly, based on the nonlinear relationship between wind speed and wind power, the distribution model of wind power prediction is established from the viewpoint of the physical mechanism. The proposed model successfully shows the complex characteristics of the wind power prediction distribution. The results show that the distribution of wind power prediction varies significantly with the point forecast of the wind speed.

Cholesterol homeostasis regulated by ABCA1 is critical for retinal ganglion cell survival

Genome-wide association studies have suggested a link between primary open-angle glaucoma and the function of ABCA1.ABCA1 is a key regulator of cholesterol efflux and the biogenesis of high-density lipoprotein(HDL) particles. Here, we showed that the POAG risk allele near ABCA1 attenuated ABCA1 expression in cultured cells. Consistently, POAG patients exhibited lower ABCA1 expression, reduced HDL, and higher cholesterol in white blood cells. Ablation of Abca1 in mice failed to form HDL, leading to elevated cholesterol levels in the retina. Counting retinal ganglion cells(RGCs) by using an artificial intelligence(AI) program revealed that Abca1-deficient mice progressively lost RGCs with age. Single-cell RNA sequencing(scRNA-seq) revealed aberrant oxidative phosphorylation in the Abca1-/-retina, as well as activation of the mTORC1 signaling pathway and suppression of autophagy. Treatment of Abca1-/-mice using atorvastatin reduced the cholesterol level in the retina,thereby improving metabolism and protecting RGCs from death. Collectively, we show that lower ABCA1 expression and lower HDL are risk factors for POAG. Accumulated cholesterol in the Abca1-/-retina causes profound aberrant metabolism, leading to a POAG-like phenotype that can be prevented by atorvastatin. Our findings establish statin use as a preventive treatment for POAG associated with lower ABCA1 expression.

Dynamic blood single-cell immune responses in patients with COVID-19

The 2019 coronavirus disease(COVID-19)outbreak caused by the SARS-CoV-2 virus is an ongoing global health emergency.However,the virus'pathogenesis remains unclear,and there is no cure for the disease.We investigated the dynamic changes of blood immune response in patients with COVID-19 at different stages by using 5'gene expression,T cell receptor(TCR),and B cell receptors(BCR)V(D)J transcriptome analysis at a single-cell resolution.We obtained single-cell mRNA sequencing(scRNA-seq)data of 341,420 peripheral blood mononuclear cells(PBMCs)and 185,430 donotypic T cells and 28,802 donotypic B cells from 25 samples of 16 patients with COVID-19 for dynamic studies.In addition,we used three control samples.We found expansion of dendritic cells(DCs),CD14+monocytes,and megakaryocytes progenitor cells(MP)/platelets and a reduction of naive CD4+T lymphocytes in patients with COVID-19,along with a significant decrease of CD8+T lymphocytes,and natural killer cells(NKs)in patients in critical condition.The type I interferon(IFN-I),mitogen-activated protein kinase(MAPK),and ferroptosis pathways were activated while the disease was active,and recovered gradually after patient conditions improved.Consistent with this finding,the mRNA level of IFN-I signal-induced gene IFI27 was significantly increased in patients with COVID-19 compared with that of the controls in a validation cohort that included 38 patients and 35 controls.The concentration of interferon-a(IFN-a)in the serum of patients with COVID-19 increased significantly compared with that of the controls in an additional cohort of 215 patients with COVID-19 and 106 controls,further suggesting the important role of the IFN-I pathway in the immune response of COVID-19.TCR and BCR sequences analyses indicated that patients with COVID-19 developed specific immune responses against SARS-CoV-2 antigens.Our study reveals a dynamic landscape of human blood immune responses to SARS-CoV-2 infection,providing clues for therapeutic potentials in treating COVID-19.

CD146 as a promising therapeutic target for retinal and choroidal neovascularization diseases

Blood vessel dysfunction causes several retinal diseases,including diabetic retinopathy,familial exudative vitreoretinopathy,macular degeneration and choroidal neovascularization in pathological myopia.Vascular endothelial growth factor(VEGF)-neutralizing proteins provide benefits in most of those diseases,yet unsolved haemorrhage and frequent intraocular injections still bothered patients.Here,we identified endothelial CD146 as a new target for retinal diseases.CD146 expression was activated in two ocular pathological angiogenesis models,a laser-induced choroid neovascularization model and an oxygeninduced retinopathy model.The absence of CD146 impaired hypoxia-induced cell migration and angiogenesis both in cell lines and animal model.Preventive or therapeutic treatment with anti-CD146 antibody AA98 significantly inhibited hypoxia-induced aberrant retinal angiogenesis in two retinal disease models.Mechanistically,under hypoxia condition,CD146 was involved in the activation of NFκB,Erk and Akt signalling pathways,which are partially independent of VEGF.Consistently,anti-CD146therapy combined with anti-VEGF therapy showed enhanced impairment effect of hypoxia-induced angiogenesis in vitro and in vivo.Given the critical role of abnormal angiogenesis in retinal and choroidal diseases,our results provide novel insights into combinatorial therapy for neovascular fundus diseases.

Genome-wide analysis identified 17 new loci influencing intraocular pressure in Chinese population

Intraocular pressure(IOP) is a major risk factor for glaucoma. Genetic determinants of intraocular pressure can provide critical insights into the genetic architecture of glaucoma and, as a result, open new avenues for therapeutic intervention. We performed a genome-wide association study and replication analysis of 8,552 Chinese participants. In the genome-wide association study, we identified 51 loci that surpassed the significance of P<9×10^(-7), and we formally replicated these loci. A combined discovery and replication meta-analysis identified 21 genome-wide loci that surpassed the genome-wide significance of P<5×10^(-8), including 4 previously reported loci: rs145063132(7 p21.2, ETV1/DGKB), rs548030386(7 q31.2, ST7 near CAV1/CAV2), rs7047871(9 p24.2, GLIS3), and rs2472494(9 q31.1, ABCA1/SLC44 A1). Of the 17 newly identified loci, five were reported to have ocular related phenotypes: PTCH2(rs7525308 in 1 p34.1), LRIF1/DRAM2(rs1282146 in 1 p13.3), COLEC11(rs201143466 in 2 p25.3),SPTBN1(rs4514918 in 2 p16.2), and CRK(rs11078446 in 17 p13.3). The genetic loci identified in this study not only increase our understanding of the genes involved in intraocular pressure but also provide important genetic markers to improve future genetic screening and drug discovery for intraocular pressure disorders.

Loss of Wtap results in cerebellar ataxia and degeneration of Purkinje cells

N^(6)-methyladenosine(m^(6)A)modification,which is achieved by the METTL3/METTL14/WTAP methyltransferase complex,is the most abundant internal mRNA modification.Although recent evidence indicates that m^(6)A can regulate neurodevelopment as well as synaptic function,the roles of m^(6)A modification in the cerebellum and related synaptic connections are not well established.Here,we report that Purkinje cell(PC)-specific WTAP knockout mice display early-onset ataxia concomitant with cerebellar atrophy due to extensive PC degeneration and apoptotic cell death.Loss of Wtap also causes the aberrant degradation of multiple PC synapses.WTAP depletion leads to decreased expression levels of METTL3/14 and reduced m^(6)A methylation in PCs.Moreover,the expression of GFAP and NF-L in the degenerating cerebellum is increased,suggesting severe neuronal injuries.In conclusion,this study demonstrates the critical role of WTAP-mediated m^(6)A modification in cerebellar PCs,thus providing unique insights related to neurodegenerative disorders.

The ER membrane protein complex subunit Emc3 controls angiogenesis via the FZD4/WNT signaling axis

The endoplasmic reticulum(ER) membrane protein complex(EMC) regulates the synthesis and quality control of membrane proteins with multiple transmembrane domains. One of the membrane spanning subunits, EMC3, is a core member of the EMC complex that provides essential hydrophilic vestibule for substrate insertion. Here, we show that the EMC subunit Emc3 plays critical roles in the retinal vascular angiogenesis by regulating Norrin/Wnt signaling. Postnatal endothelial cell(EC)-specific deletion of Emc3 led to retarded retinal vascular development with a hyperpruned vascular network, the appearance of bluntended, aneurysm-like tip endothelial cells(ECs) with reduced numbers of filopodia and leakage of erythrocytes at the vascular front. Diminished tube formation and cell proliferation were also observed in EMC3 depleted human retinal endothelial cells(HRECs). We then discovered a critical role for EMC3 in expression of FZD4 receptor of β-catenin signaling using RNA sequencing, real-time quantitative PCR(RT-q PCR) and luciferase reporter assay. Moreover, augmentation of Wnt activity via lithium chloride(Li Cl) treatment remarkably enhanced β-catenin signaling and cell proliferation of HRECs. Additionally, Li Cl partially reversed the angiogenesis defects in Emc3-c KO mice. Our data reveal that Emc3 plays essential roles in angiogenesis through direct control of FZD4 expression and Norrin/β-catenin signaling.

Dynamic human retinal pigment epithelium(RPE)and choroid architecture based on single-cell transcriptomic landscape analysis

The retinal pigment epithelium(RPE)and choroid are located behind the human retina and have multiple functions in the human visual system.Knowledge of the RPE and choroid cells and their gene expression profiles are fundamental for understanding retinal disease mechanisms and therapeutic strategies.Here,we sequenced the RNA of about 0.3 million single cells from human RPE and choroids across two regions and seven ages,revealing regional and age differences within the human RPE and choroid.Cell–cell interactions highlight the broad connectivity networks between the RPE and different choroid cell types.Moreover,the transcription factors and their target genes change during aging.The coding of somatic variations increases during aging in the human RPE and choroid at the single-cell level.Moreover,we identified ELN as a candidate for improving RPE degeneration and choroidal structure during aging.The mapping of the molecular architecture of the human RPE and choroid improves our understanding of the human vision support system and offers potential insights into the intervention targets for retinal diseases.

Defective EMC1 drives abnormal retinal angiogenesis via Wnt/β-catenin signaling and may be associated with the pathogenesis of familial exudative vitreoretinopathy

Endoplasmic reticulum(ER)membrane protein complex(EMC)is required for the co-translational insertion of newly synthesized multi-transmembrane proteins.Compromised EMC function in different cell types has been implicated in multiple diseases.Using inducible genetic mouse models,we revealed defects in retinal vascularization upon endothelial cell(EC)specific deletion of Emc1,the largest subunit of EMC.Loss of Emc1 in ECs led to reduced vascular progression and vascular density,diminished tip cell sprouts,and vascular leakage.We then performed an unbiased transcriptomic analysis on human retinal microvascular endothelial cells(HRECs)and revealed a pivotal role of EMC1 in theβ-catenin signaling pathway.Further in-vitro and in-vivo experiments proved that loss of EMC1 led to compromisedβ-catenin signaling activity through reduced expression of Wnt receptor FZD4,which could be restored by lithium chloride(LiCl)treatment.Driven by these findings,we screened genomic DNA samples from familial exudative vitreoretinopathy(FEVR)patients and identified one heterozygous variant in EMC1 that co-segregated with FEVR phenotype in the family.In-vitro expression experiments revealed that this variant allele failed to facilitate the expression of FZD4 on the plasma membrane and activate theβ-catenin signaling pathway,which might be a main cause of FEVR.In conclusion,our findings reveal that variants in EMC1 gene cause compromisedβ-catenin signaling activity,which may be associated with the pathogenesis of FEVR.

Evaluation of FGF10 as a candidate gene for high myopia in a Han Chinese population

Background:Fibroblast growth factor 10(FGF10)is implicated in the growth and development of the eye.Four singles nucleotide polymorphisms(SNPs)in the FGF10 gene(including rs1384449,rs339501,rs12517396 and rs10462070)were found to be associated with extreme myopia(EM,refractive error≤−10.0 diopters)in Japanese and Chinese Taiwan population.This case-control association study was conducted to explore the relationship between these four SNPs and high myopia in a western Chinese population.Methods:A total of 869 high myopia patients(HM,including 485 EM patients)and 899 healthy controls were recruited.These four SNPs were genotyped using the ABI SNaPshot method.Five genetic models(allelic,homozygous,heterozygous,dominant,and recessive)were applied to further evaluate the possible correlation between the SNPs and high myopia.The linkage-disequilibrium block(LD)structure was tested by Haploview Software.Results:In our study,no statistically significant differences were found between HM/EM patients and controls after Bonferroni multiple-correction(P>0.05)in the allele frequencies of these four SNPs in the FGF10 gene.We further found that rs12517396AA and rs10462070GG carriers showed a decreased risk of HM/EM compared with rs12517396AC+CC and rs10462070GA+AA carriers(P=0.045,OR=0.366;P=0.021,OR=0.131;P=0.03,OR=0.341;P=0.015,OR=0.122;respectively).Additionally,rs12517396AA and rs10462070GG carriers showed the same decreased risk of HM/EM compared with rs12517396CC and rs10462070AA carriers(P=0.048,OR=0.370;P=0.023,OR=0.133;P=0.032,OR=0.346;P=0.017,OR=0.126).However,these significant associations between rs12517396/rs10462070 and HM/EM disappeared after Bonferroni multiple-correction(P>0.05).Conclusion:Our findings indicate that rs12517396 and rs10462070 had marginal association with HM and EM.The other two common polymorphisms in FGF10 unlikely have significant effects in the genetic predisposition to HM/EM in western Chinese population.Further replication studies are needed to validate our findings in both animal models and human genetic epidemiologic studies.

Deep Sc-RNA sequencing decoding the molecular dynamic architecture of the human retina

The human retina serves as a light detector and signals transmission tissue.Advanced insights into retinal disease mechanisms and therapeutic strategies require a deep understanding of healthy retina molecular events.Here,we sequenced the m RNA of over 0.6 million single cells from human retinas across six regions at nine different ages.Sixty cell sub-types have been identified from the human mature retinas with unique markers.We revealed regional and age differences of gene expression profiles within the human retina.Cell-cell interaction analysis indicated a rich synaptic connection within the retinal cells.Gene expression regulon analysis revealed the specific expression of transcription factors and their regulated genes in human retina cell types.Some of the gene’s expression,such as DKK3,are elevated in aged retinas.A further functional investigation suggested that over expression of DKK3 could impact mitochondrial stability.Overall,decoding the molecular dynamic architecture of the human retina improves our understanding of the vision system.

Variants in the Wnt co-receptor LRP6 are associated with familial exudative vitreoretinopathy

Familial exudative vitreoretinopathy(FEVR),an inherited eye disease,is characterized by abnormal retinal vascular development,such as neovascularization,vitreous hemorrhage,exudation,and retinal detachment(Criswick and Schepens,1969;Robitaille et al.,2002).FEVR is inherited as autosomal dominant,autosomal recessive,and X-linked patterns(de Crecchio et al.,1998).