Chromosome-level genome assembly of a regenerable maize inbred line A188

Background: The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results: Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions: The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues

Study of efficacy and antibody duration to fourth-dose booster of Ad5-nCoV or inactivated SARS-CoV-2 vaccine in Chinese adults: a prospective cohort study

IntroductionChina experienced a record surge of coronavirus disease 2019 cases in December 2022, during the pandemic.MethodsWe conducted a randomized, parallel-controlled prospective cohort study to evaluate efficacy and antibody duration after a fourth-dose booster with Ad5-nCoV or inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine.ResultsA total of 191 participants aged ≥18 years who had completed a three-dose regimen of the inactivated SARS-CoV-2 vaccine 6 months earlier were recruited to receive the intramuscular Ad5-nCoV booster or the inactivated SARS-CoV-2 vaccine. The Ad5-nCoV group had significantly higher antibody levels compared with the inactivated vaccine group at 6 months after the fourth vaccination dose. After the pandemic, the breakthrough infection rate for the Ad5-nCoV and the inactivated vaccine groups was 77.89% and 78.13%, respectively. Survival curve analysis (p = 0.872) and multivariable logistic regression analysis (p = 0.956) showed no statistically significant differences in breakthrough infection between the two groups.DiscussionCompared with a homologous fourth dose, a heterologous fourth dose of Ad5-nCoV elicited a higher immunogenic response in healthy adults who had been immunized with three doses of inactivated vaccine. Nevertheless, the efficacy of the two vaccine types was equivalent after the pandemic

Chromosome-level genome assembly of a regenerable maize inbred line A188.

BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants

Regulatory network of genes associated with stimuli sensing, signal transduction and physiological transformation of appressorium in Magnaporthe oryzae

Rice blast caused by Magnaporthe oryzae is the most destructive disease affecting the rice production (Oryza sativa), with an average global loss of 10–30% per annum. Recent reports have indicated that the fungus also inflicts blast disease on wheat (Triticum aestivum) posing a serious threat to the wheat production. Due to its easily detected infectious process and manoeuvrable genetic manipulation, M. oryzae is considered a model organism for exploring the molecular mechanism underlying fungal pathogenicity during the pathogen–host interaction. M. oryzae utilises an infectious structure called appressorium to breach the host surface by generating high turgor pressure. The appressorium development is induced by physical and chemical cues which are coordinated by the highly conserved cAMP/PKA, MAPK and calcium signalling cascades. Genes involved in the appressorium development have been identified and well studied in M. oryzae, a summary of the working gene network linking stimuli sensing and physiological transformation of appressorium is needed. This review provides a comprehensive discussion regarding the regulatory networks underlying appressorium development with particular emphasis on sensing of appressorium inducing stimuli, signal transduction, transcriptional regulation and the corresponding developmental and physiological responses. We also discussed the crosstalk and interaction of various pathways during the appressorium development

Highly Conductive Hierarchical TiO2 Micro-Sheet Enables Thick Electrodes in Sodium Storage

TiO2-based materials are considered to be the promising anodes of sodium-ion batteries (NIBs) because of their high safety and good stability. However, their low specific capacity and high safety operating voltage plateau impose a severe challenge for high energy density batteries. Herein, interconnected micro-sheets consisting of carbon nanotubes and sulfur doped TiO2 (CNT/S-TiO2) are synthesized via an ultrasonic process and subsequent calcination, enabling the fabrication of high-performance material. The utilization of SWCNT overcomes the structure instabilities during electrode preparation of thick electrodes. The incorporation of SWCNT and sulfur dopants in the CNT/S-TiO2 composite not only enhances conductivity but also improves ion transport dynamics, resulting in rapid charge delivery and high specific capacity at the thick electrode level. Consequently, CNT/S-TiO2 demonstrates excellent rate performance (from 0.3 to 15 C, with 72.4% capacity retention) and long cycling stability (10000 cycles at a load of 1.96 mg cm−2). More importantly, the high S-TiO2 content (90%) in the thick electrode (21.2 mg cm−2) achieves a high areal capacity retention of 3.4 mA h cm−2 after 100 cycles, which surpasses the actual application requirements

A simple automated device for children's renal biopsy: advantage in obtaining more tissue

Sufficient tissue yield is essential for renal biopsy. We have developed a simple automated renal biopsy device (Chen device) that constantly obtains more tissue. Since the Bard device is extensively used around the world, we compared our device with the Bard device. Pediatric patients were biopsied with either the Chen (n=247) or Bard (n=200) devices. No major complications were encountered and the incidence of minor complications was comparable between two devices. However, the average length of tissue obtained by the Chen device per biopsy (1.78+/-0.73 cm) was significantly longer than that obtained by the Bard device (1.23+/-0.45 cm). Accordingly, 61.94% of biopsies with the Chen device had 20 or more glomeruli, whereas only 18% of biopsies with the Bard device had this number (p<0.001). Thus, the Chen device has the advantage of obtaining more renal tissue per biopsy while being equally efficient and safe as the Bard device

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection

Abstract Background Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited. Results Here, we explored gene expression divergence between a japonica rice cultivar Nipponbare and an indica rice cultivar 93–11 in response to invasion by the filamentous ascomycete fungus Magnaporthe oryzae (Pyricularia oryzae), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of cis-regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence. Conclusion We proposed that variation in the expression patterns of these orthologous genes mediated by cis-regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to M. oryzae infection

Factors Correlating to the Development of Hepatitis C Virus Infection in Hemodialysis Patients—Findings Mainly from Asiatic Populations: A Systematic Review and Meta-Analysis

Hemodialysis is an effective replacement therapy for chronic renal failure patients. In recent decades, the number of hemodialysis patients has grown rapidly and some measures for preventing blood-borne diseases have been implemented, but hepatitis C virus (HCV) infection remains a significant problem. The meta-analysis published in 2009 on HCV infection-related factors was based on localized study objects, and some additional studies have been published since 2009; however, the contribution of these factors remains under dispute. Our study pooled the odds ratios (ORs) or mean standard deviations (MDs) with 95% confidence intervals (CIs) and analyzed sensitivity using Review Manager 5.1 software (5.1 version Copenhagen: The Nordic Cochrane Centre; 2011) by searching data in the PubMed, Elsevier, Springer, Wiley, and EBSCO databases. Spearman correlation analysis was performed using the SPSS package. In our meta-analysis, 1715 HCV-infected hemodialysis patients and 7093 non-HCV-infected hemodialysis patients from 44 studies were analyzed. The pooled ORs with 95% CIs were: histories of blood transfusion, 4.30 (3.11, 5.96); weekly hemodialysis times &gt; 2, 6.00 (3.25, 11.06); kidney transplantation, 5.80 (3.95, 8.52); hemodialysis units &gt; 2, 6.90 (2.42, 19.68); shared hemodialysis devices, 5.00 (2.35, 10.65); and drug addiction, 4.73 (1.54, 14.47). The pooled MDs with 95% CIs were duration of hemodialysis (months) 27.48 (21.67, 33.30). There was a positive correlation between duration of hemodialysis and the HCV infection rate (p &lt; 0.01). Hemodialysis patients, especially from Asia, with shared hemodialysis devices, hemodialysis units &gt; 2, blood transfusion, kidney transplantation, and drug addiction were at increased risk of HCV infection. The HCV infection rate increased with the duration of hemodialysis. High-risk hemodialysis patients should be monitored and receive timely screening