The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae

Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we show that rice (Oryza sativa) mesophyll cells are prone to DNA double-stranded breaks (DSBs) in response to ZJ173, a strain of Xanthomonas oryzae pv. oryzae (Xoo). The DSB signal transducer ataxia telangiectasia mutated (ATM), but not the ATM and Rad3-related branch, confers resistance against Xoo. Mechanistically, the MRE11-ATM module phosphorylates suppressor of gamma response 1 (SOG1), which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo infection. Intriguingly, overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining (NHEJ) pathway to the alternative NHEJ and homologous recombination pathways at Xoo-induced DSBs. The enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression lines. Overall, the MRE11-ATM-SOG1 pathway serves as a prime example of plant-pathogen interactions that occur via host non-specific recognition. The function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 expression quantitative trait loci associated with the expression of 7787 and 9361 eGenes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5-a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

mRNA cleavage by 21-nucleotide phasiRNAs determines temperature-sensitive male sterility in rice

Temperature-sensitive male sterility is one of the core components for hybrid rice (Oryza sativa) breeding based on the 2-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) causes temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in the ago1d mutant remain unknown. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multiomics analysis of small RNA (sRNA), degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt sRNA species in rice anthers and are sensitive to low temperature and markedly downregulated in the ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as Earlier Degraded Tapetum 1 (EDT1), Tapetum Degeneration Retardation (TDR), OsPCF5, and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss of function of 21-nt phasiRNAs can result in upregulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in 2-line hybrid rice breeding in the future.

[Quality control of perioperative management after radical surgery for locally advanced gastric cancer]

Gastric cancer is a common malignant tumor in China. Most gastric cancer patients are already in the locally advanced stage when they seek medical treatment. Radical surgery is the main treatment for gastric cancer. The quality control of postoperative perioperative management is of great significance in improving the surgical treatment effect and the quality of life of patients. This article systematically summarizes seven aspects, including diet and nutrition management, antimicrobial drug management, pain management, prophylactic anticoagulation management, airway management, postoperative complication management, and discharge and follow-up management, establishes clear quality standards, and achieves the goals of reducing postoperative complications, standardizing perioperative medication use, reducing hospitalization time and costs, thereby reducing patient burden and improving the economic and social benefits of medical institutions.

Programmable RNA N6 -methyladenosine editing with CRISPR/dCas13a in plants

N6 -methyladenonsine (m6 A) is the most prevalent internal modification of messenger RNA (mRNA) and plays critical roles in mRNA processing and metabolism. However, perturbation of individual m6 A modification to reveal its function and the phenotypic effects is still lacking in plants. Here, we describe the construction and characterization of programmable m6 A editing tools by fusing the m6 A writers, the core catalytic domain of the MTA and MTB complex, and the AlkB homologue 5 (ALKBH5) eraser, to catalytically dead Cas13a (dCas13a) to edit individual m6 A sites on mRNAs. We demonstrated that our m6 A editors could efficiently and specifically deposit and remove m6 A modifications on specific RNA transcripts in both Nicotiana benthamiana and Arabidopsis thaliana. Moreover, we found that targeting SHORT-ROOT (SHR) transcripts with a methylation editor could significantly increase its m6 A levels with limited off-target effects and promote its degradation. This leads to a boost in plant growth with enlarged leaves and roots, increased plant height, plant biomass, and total grain weight in Arabidopsis. Collectively, these findings suggest that our programmable m6 A editing tools can be applied to study the functions of individual m6 A modifications in plants, and may also have potential applications for future crop improvement.

A centromere map based on super pan-genome highlights the structure and function of rice centromeres

Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.

Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome

Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for the development of high-yield and thermotolerant rice varieties.

Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering

The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.

A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants

Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations. Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that ∼90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics.

Comparative Metabolomics Combined with Physiological Analysis Revealed Cadmium Tolerance Mechanism in Indica Rice (Oryza sativa L.)

Cadmium (Cd) pollution reduces rice production and quality, putting food security and human health at risk. We conducted comparative physiology and metabolomic analyses in two indica rice ('NH199' and 'NH224') to elucidate the Cd-tolerance mechanism. Cd hampered rice growth, induced oxidative stress, and changed the metabolomics profiling of the root. The biochemical and physiological analysis demonstrated that NH224 exhibited a more potent Cd-tolerance ability than NH199. Cd was primarily distributed in root, and NH224 had a lower Cd translocation factor than NH199 by about 24%. The metabolomic analysis revealed 180 and 177 differentially accumulated metabolites between Cd-stressed seedlings and the controls in NH224 and NH199, respectively. In NH224, amino acids biosynthesis, hormone metabolism, lipids-related metabolism, phenylalanine metabolism, and phenylpropanoid biosynthesis pathways were more active and highly associated with antioxidant defense system, biosynthesis of the cell wall and phytochelatins, and maintenance of plasma membrane stability. These findings provide insights into the metabolic profiles of rice following Cd stress and the screening and breeding of Cd-tolerant rice varieties.

Enhancement of Heat and Drought Stress Tolerance in Rice by Genetic Manipulation: A Systematic Review

As a result of global warming, plants are subjected to ever-increasing abiotic stresses including heat and drought. Drought stress frequently co-occurs with heat stress as a result of water evaporation. These stressors have adverse effects on crop production, which in turn affects human food security. Rice is a major food resource grown widely in crop-producing regions throughout the world. However, increasingly common heat and drought stresses in growth regions can have negative impacts on seedling morphogenesis, reproductive organ establishment, overall yield, and quality. This review centers on responses to heat and drought stress in rice. Current knowledge of molecular regulation mechanisms is summarized. We focus on approaches to cope with heat and drought stress, both at the genetic level and from an agricultural practice perspective. This review establishes a basis for improving rice stress tolerance, grain quality, and yield for human benefit.

Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication

The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F _ST analysis based on SVs (SV-F _ST) while not by F _ST analysis based on SNPs (SNP-F _ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.

A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Complex biological processes such as plant growth and development are often under the control of transcription factors that regulate the expression of large sets of genes and activate subordinate transcription factors in a cascade-like fashion. Here, by screening candidate photosynthesis-related transcription factors in rice, we identified a DREB (Dehydration Responsive Element Binding) family member, OsDREB1C, in which expression is induced by both light and low nitrogen status. We show that OsDREB1C drives functionally diverse transcriptional programs determining photosynthetic capacity, nitrogen utilization, and flowering time. Field trials with OsDREB1C-overexpressing rice revealed yield increases of 41.3 to 68.3% and, in addition, shortened growth duration, improved nitrogen use efficiency, and promoted efficient resource allocation, thus providing a strategy toward achieving much-needed increases in agricultural productivity.

A super pan-genomic landscape of rice

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

[Characteristics and risk factors of functional constipation in children aged 0-4 years in Xi 'an]

Objective: To investigate the epidemiology, characteristics and risk factors of functional constipation (FC) in children aged 0-4 years in Xi'an. Methods: From October, 2020 to June, 2021, a prevalence survey was conducted among 2 615 children aged 0-4 years in Xi'an by group sampling. The related factors of FC were investigated by questionnaire designed based on Rome Ⅳ diagnostic criteria.The children were divided into FC group and non-FC group. The prevalence, symptoms and signs of FC were analyzed, and its risk factors were analyzed by multivariate Logistic regression. Results: A total of 2 985 valid questionnaires were handed out, and 2 711 (90.8%) were received back. A total of 2 615 questionnaires were valid, with an effective rate of 96.5%. There were 1 338 males (51.2%) and 1 277 females (48.8%). There were 260 cases in FC group and 2 355 cases in non-FC group. The prevalence of FC in children aged 0-4 years in Xi 'an was 10.6%.There were significant differences in FC prevalence among children of different ages and sex (χ²=14.58,4.39, both P<0.05), but not in urban or rural residence (χ²=3.29, P=0.070). The main symptoms of FC group in the last month were large-diameter feces (73.5%, 191/260), painful defecation or dry and hard defecation (65.8%, 171/260). In the last month, FC group had higher incidences of the Bristol type 1, 2 and 3 stool, fecal retention, prolonged defecation, abdominal pain and incomplete defecation compared with non-FC group, with statistical significance (all P<0.05). Parental history of childhood constipation (OR=2.13, 95%CI 1.55-2.92), fever in the last month (OR=1.86, 95%CI 1.32-2.63), history of constipation (OR=3.24, 95%CI 2.46-4.26) and taking probiotics in the last month (OR=1.45, 95%CI 1.11-1.91) were risk factors of FC in children aged 0-4 years. Stratified with age, the results showed that complementary feeding earlier than 5 months of age or later than 6 months of age (OR=2.42, 95%CI 1.13-5.20), dry stools during the complementary feeding (OR=11.27, 95%CI 5.15-24.66), history of constipation (OR=2.29, 95%CI 1.23-4.29) and taking probiotics in the last month (OR=1.88, 95%CI 1.10-3.23) were risk factors of FC in children aged 0-<1 year, and breastfeeding (OR=0.53, 95%CI 0.29-0.94) was a protective factor of FC in children aged 0-<1 year. Family members' recent constipation history (OR=2.02, 95%CI 1.06-3.85) and past history of constipation (OR=3.06, 95%CI 1.74-5.38) were FC risk factors for children aged 1-<2 years. Parental history of childhood constipation (OR=3.12, 95%CI 2.00-4.85), frequency of eating vegetables less than 3 times per week (OR=3.28, 95%CI 2.00-5.38), history of constipation (OR=3.66, 95%CI 2.42-5.53) and taking antibiotics in the last month (OR=1.65, 95%CI 1.06-2.55) were risk factors for FC in children aged 2-4 years. Conclusions: FC in children aged 0-4 years in Xi'an is mainly manifested with large-diameter feces and painful defecation or dry and hard defecation in the last month. It is associated with a variety of risk factors, which are different in different age groups.

[P4HA2 promotes occurrence and progression of liver cancer by regulating the PI3K/Akt/mTOR signaling pathway]

OBJECTIVE

To investigate the role of proline 4-hydroxylase Ⅱ (P4HA2) in the occurrence and progression of liver cancer.

METHODS

GEPIA and Human Protein Atlas database were used to predict the expression of P4HA2 in hepatocellular carcinoma (HCC), and K-M plotter online database was used to analyze the relationship between P4HA2 expression and the prognosis of HCC. We also examined the expressions of P4HA2 in HCC cells and normal hepatocytes using qRT-PCR and Western blotting. With lentivirus-mediated RNA interference, P4HA2 expression was knocked down in hepatoma SNU-449 and Hep-3B cells, and the changes in cell proliferation, migration and invasion were assessed using cell counting kit-8 (CCK-8) assay, colony formation test, scratch test and Transwell assay. The changes in the expressions of epithelial-mesenchymal transition (EMT) and PI3K/Akt/mTOR signal pathway-related proteins were detected using Western blotting.

RESULTS

Online database analysis showed that the expression of P4HA2 was significantly higher in HCC tissues than in normal liver tissues (P < 0.05). The expression levels of P4HA2 mRNA and protein were also significantly higher in HCC cell lines than in normal hepatocytes (P < 0.01). Lentivirus-mediated RNA interference of P4HA2 significantly lowered the expression levels of P4HA2 mRNA and protein in the hepatoma cells (P < 0.05) and caused obvious inhibition of cell proliferation, migration and invasion. P4HA2 knockdown significantly increased the expression of E-cadherin protein, lowered the expressions of N-cadherin and Snail, and obviously decreased the expressions of phosphorylated PI3K, AKT and mTOR (P < 0.05).

CONCLUSION

P4HA2 enhances the proliferation, migration, invasion, and EMT of hepatoma cells by activating the PI3K/Akt/mTOR signaling pathway to promote the occurrence and progression of liver cancer.

Twenty years of plant genome sequencing: achievements and challenges

Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes.

OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice

Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.

Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.

Natural alleles of a uridine 5'-diphospho-glucosyltransferase gene responsible for differential endosperm development between upland rice and paddy rice

Traditional upland rice generally exhibits insufficient grains resulting from abnormal endosperm development compared to paddy rice. However, the underlying molecular mechanism of this trait is poorly understood. Here, we cloned the uridine 5'-diphospho (UDP)-glucosyltransferase gene EDR1 (Endosperm Development in Rice) responsible for differential endosperm development between upland rice and paddy rice by performing quantitative trait loci analysis and map-based cloning. EDR1 was highly expressed in developing seeds during grain filling. Natural variations in EDR1 significantly reduced the UDP-glucosyltransferase activity of EDR1^YZN compared to EDR1^YD1 , resulting in abnormal endosperm development in the near-isogenic line, accompanied by insufficient grains and changes in grain quality. By analyzing the distribution of the two alleles EDR1^YD1 and EDR1^YZN among diverse paddy rice and upland rice varieties, we discovered that EDR1 was conserved in upland rice, but segregated in paddy rice. Further analyses of grain chalkiness in the alleles of EDR1^YD1 and EDR1^YZN varieties indicated that rice varieties harboring EDR1^YZN and EDR1^YD1 preferentially showed high chalkiness, and low chalkiness, respectively. Taken together, these results suggest that the UDP-glucosyltransferase gene EDR1 is an important determinant controlling differential endosperm development between upland rice and paddy rice.

Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)

Nitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll content, and leaf length) of the 225-rice-variety natural population from the Rice 3K Sequencing Project across normal nitrogen (NN) and low nitrogen (LN) environments. The LNGR phenotypic difference between NN and LN levels was used for gene analysis using a genome-wide association study (GWAS) combined with 111,205 single-nucleotide polymorphisms (SNPs) from the available sequenced data from the 3K project. We obtained a total of 56 significantly associated SNPs and 4 candidate genes for 4 LNGR traits. Some loci were located in the candidate regions, such as MYB61, OsOAT, and MOC2. To further study the role of candidate genes, we conducted haplotype analyses to identify the elite germplasms. Moreover, several other plausible candidate genes encoding LN-related or NUE proteins were worthy of mining. Our study provides novel insight into the genetic control of LNGR and further reveals some related novel haplotypes and potential genes with phenotypic variation in rice.

A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice

Grain size is one of the most important factors that control rice yield, as it is associated with grain weight (GW). To date, dozens of rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Here, the quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB) and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW. RNA sequencing, gene expression quantification, dual-luciferase reporter assays, chromatin immunoprecipitation-quantitative PCR, and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3. OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter, covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells. Furthermore, we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing. Taken together, our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, providing a potential target for the improvement of rice yield.

What is an appropriate caesarean delivery rate for China: a multicentre survey

Objective

To assess the current status of caesarean delivery (CD) in China, propose reference CD rates for China overall, and by regions, investigate the main indications for CDs and identify possible areas for safe reduction.

Design

A multicentre cross‐sectional study.

Setting

A total of 94 hospitals across 23 provinces in China.

Population

A total of 73 977 randomly selected deliveries.

Methods

We used a modified Robson classification to characterise CDs in subgroups and by regions, and the World Health Organization (WHO) C‐Model to calculate reference CD rates.

Main outcome measures

CD rates in China.

Results

In 2015–2016, the overall CD rate in China was 38.9% (95% CI 38.6–39.3%). Considering the obstetric characteristics of the population, the multivariable model‐based reference CD rate was estimated at 28.5% (95% CI 28.3–28.8%). Accordingly, an absolute reduction of 10.4% (or 26.7% relative reduction) may be considered. The CD rate varied substantially by region. Previous CD was the most common indication in all regions, accounting for 38.2% of all CDs, followed by maternal request (9.8%), labour dystocia (8.3%), fetal distress (7.7%) and malpresentation (7.6%). Overall, 12.7% of women had prelabour CDs, contributing to 32.8% of the total CDs.

Conclusions

Nearly 39% of births were delivered by caesarean in China but a reduction of this rate by a quarter may be considered attainable. Repeat CD contributed more than one‐third of the total CDs. Given the large variation in maternal characteristics, region‐specific or even hospital‐specific reference CD rates are needed for precision management of CD.

Tweetable abstract

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

Linked article This article is commented on by M Varner, p. 148 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16953.

Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BACKGROUND

Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.

RESULTS

In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.

CONCLUSION

The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BACKGROUND

Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.

RESULTS

In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.

CONCLUSION

The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

OsbHLH98 regulates leaf angle in rice through transcriptional repression of OsBUL1

Leaf angle is an important agronomic trait in cereals that helps determine plant yield by affecting planting density. However, the regulation mechanism of leaf angle remained elusive. Here, we show that OsbHLH98, a rice bHLH transcription factor, negatively regulates leaf angle. osbhlh98 mutant leaves formed a larger leaf angle, whereas transgenic plants overexpressing OsbHLH98 exhibited a slight reduction in leaf angle. We determined that the changes in leaf angle resulted from increased number and size of parenchyma cells on the adaxial side of the lamina joint in osbhlh98 mutants. Experiments using reporter constructs showed that OsbHLH98 is expressed on the adaxial side of lamina joints, consistent with its proposed function in regulating leaf angle. Furthermore, we established by chromatin immunoprecipitation and CUT&RUN that OsBUL1 is a direct downstream target of OsbHLH98. Transactivation assays and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis indicated that OsbHLH98 represses OsBUL1 transcription. Our results demonstrate that OsbHLH98 negatively regulates leaf angle by counteracting brassinosteroid-induced cell elongation via the repression of OsBUL1 transcription. The characterization of OsbHLH98 and its role in determining leaf angle will lay the foundation to develop the ideal plant architecture for adaptation to high planting density.

Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

BACKGROUND

Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses.

METHODS

Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany.

RESULTS

Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.

CONCLUSIONS

This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

BACKGROUND

Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.

RESULT

Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.

CONCLUSIONS

The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

BACKGROUND

Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.

RESULT

Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.

CONCLUSIONS

The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Inhibition of CD44 attenuates pressure overload-induced cardiac and lung inflammation, fibrosis, and heart failure progression

Background

Inflammation contributes to heart failure (HF) development and progression. CD44 is a member of the hyaluronate receptor family of cell adhesion molecules, which regulates tissue inflammation and fibrosis through modulating macrophage and lymphocyte migration and homing in several diseases. Here we evaluated the role and cellular mechanism of CD44 in regulating transverse aortic constriction (TAC)-induced HF development and progression in mice.

Methods and results

C57/B6 background CD44 KO and wild type mice (6–8 weeks) were subjected to TAC to evaluate the effect of CD44 on the development of TAC-induced LV hypertrophy and cardiac dysfunction. Due to the rapid response to TAC, Balb/c mice (6–8 weeks) were used to determine the effect of CD44 on the progression of TAC-induced congestive heart failure. We found that CD44 expression is dramatically increased in left ventricular (LV) tissues obtained from HF patients and mice. While CD44 gene knockout (KO) has no detectable effect on cardiac structure and function under control conditions, CD44 KO mice were protected from TAC-induced LV inflammation, fibrosis, hypertrophy, dysfunction, and lung remodeling as compared with wild type mice. In addition, we found that inhibition of CD44 signaling with blocking antibodies (Abs) significantly attenuated the transition from LV failure to lung remodeling, and right ventricular hypertrophy in mice with existing HF.

Conclusions

These data identify an important role of CD44 in attenuating cardiac and lung inflammation, fibrosis, HF development, and HF progression, suggesting that inhibition of CD44 signaling may be useful in preventing and treating HF.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Chinese National Natural Science Foundation Grants and American Heart Association

[Clinical and laboratory characteristics in patients with myeloid neoplasms complicated with clonal T large granular lymphocyte proliferation]

Objective: To analyze the clinical manifestations and laboratory features in patients with myeloid neoplasms complicated with clonal T large granular lymphocyte (T-LGL) proliferation. Methods: The clinical data of 5 patients with myeloid neoplasms complicated with clonal T-LGL proliferation from November 2017 to November 2018 in Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College were analyzed retrospectively. Results: The median age was 60 years old. All patients had a history of abnormal peripheral blood cell counts for over 6 months. The absolute lymphocyte count in peripheral blood was less than 1.0×10(9)/L. In addition to the typical T-LGL phenotype, the immunophenotype was heterogenous including CD4(+)CD8(-) in 2 patients, the other 3 CD4(-)CD8(+). Four patients were αβ type T cells, the other one was γδ type. STAT3 mutation was detected in 1 patient by next-generation sequencing, the other 4 cases were negative. Conclusions: Clonal T-LGL proliferation with myeloid neoplasm develops in an indolent manner, mainly in elderly patients. Hemocytopenia is the most common manifestation. The diagnosis of T-LGL proliferation does not have specific criteria, that it should be differentiated from other T cell proliferative disorders, such as T-cell clones of undetermined significance. STAT3 or STAT5b mutation may help distinguish.

Natural variation in the promoter of TGW2 determines grain width and weight in rice

Understanding the genetic basis of natural variation in grain size among diverse rice varieties can help breeders develop high-yielding rice cultivars. Here, we report the discovery of qTGW2, a new semidominant quantitative trait locus for grain width and weight. The corresponding gene, TGW2, encodes CELL NUMBER REGULATOR 1 (OsCNR1) localized to the plasma membrane. A single nucleotide polymorphism (SNP) variation 1818 bp upstream of TGW2 is responsible for its different expression, leading to alteration in grain width and weight by influencing cell proliferation and expansion in glumes. TGW2 interacts with KRP1, a regulator of cell cycle in plants, to negatively regulate grain width and weight. Genetic diversity analysis of TGW2 in 141 rice accessions revealed it as a breeding target in a selective sweep region. Our findings provide new insights into the genetic mechanism underlying grain morphology and grain weight, and uncover a promising gene for improving rice yield.

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

Plant architecture is a complex agronomic trait and a major factor of crop yield, which is affected by several important hormones. Strigolactones (SLs) are identified as a new class hormoneinhibiting branching in many plant species and have been shown to be involved in various developmental processes. Genetical and chemical modulation of the SL pathway is recognized as a promising approach to modify plant architecture. However, whether and how the genes involved in the SL pathway could be utilized in breeding still remain elusive. Here, we demonstrate that a partial loss-of-function allele of the SL biosynthesis gene, HIGH TILLERING AND DWARF 1/DWARF17 (HTD1/D17), which encodes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), increases tiller number and improves grain yield in rice. We found that the HTD1 gene had been widely utilized and co-selected with Semidwarf 1 (SD1), both contributing to the improvement of plant architecture in modern rice varieties since the Green Revolution in the 1960s. Understanding how phytohormone pathway genes regulate plant architecture and how they have been utilized and selected in breeding will lay the foundation for developing the rational approaches toward improving crop yield.

FRI0261 DIFFERENTIAL EXPRESSION OF PERIPHERAL CD4+ T CELLS IN PATIENTS WITH SYSTEMIC SCLEROSIS AND MIXED CONNECTIVE TISSUE DISEASE

Background:

The CD4+T cell subsets plays an important role in its pathogenesis, and its new research are constantly being published, but its specific changes between SSc and MCTD are still unclear.

Objectives:

The aim of the present study was to explore the absolute numbers of CD4+T subsets in peripheral blood(PB) of patients with SSc and MCTD using our modified flow cryometric method and investigate the role in the pathogenesis of both.

Methods:

The PB samples from 54 patients with SSc, 51 patients with MCTD as well as 30 healthy control subjects were analyzed for lymphocyte subsets using flow cytometry. Of these patients, 19 had pulmonary involvement, including 9 patients with SSc and 10 patients with MCTD. Using directly the percentages from flow cytometry combined with internal standard beads calculated absolute number of peripheral lymphocyte subsets from the subjects in each group.

Results:

Although there were some changes among CD4+T cell subsets in PB from these SSc patients and MCTD patients, the major alteration was the reductions of Treg cells. Compared with the normal controls, the absolute number of CD4+CD25+FOXP3+Treg cells were significantly decreased in SSc patients and MCTD patients, and the absolute number of Th1 cells in MCTD patients is also significantly reduced. Notably, the absolute numbers of Th17 and Th2 cells were not different from those of normal controls, but the ratios of Th17/Treg in SSc patients and MCTD patients were significantly higher, causing by insufficient number of Treg cells (Fig 1). In addition, in patients with pulmonary involvement, we found that the absolute number of Treg cells was significantly reduced in patients with MCTD, while the absolute number of Th2 cells and Th17 cells was significantly reduced in patients with SSc(Fig 2).

Fig 1.

Comparison of the levels of CD4+T lymphocyte subsets in SSc patients, MCTD patients and healthy controls: (A) The absolute number of peripheral Th1 cells in patients with MCTD was significantly reduced; (B and C) There was no significant difference in the absolute number of Th2 cells in peripheral blood of different subjects; (D and E) The ratio of Th17/Treg cells in PB of patients with SSc and MCTD were significantly higher.*P< 0.05; **P< 0.01; ***P< 0.001.

Conclusion:

The number of peripheral Treg cells in patients with SSc and MCTD was significantly reduced, suggesting that that SSc and MCTD progression is associated with the imbalances between pro-inflammation cells to anti-inflammation Treg cells. In addition, we also found that the decrease in peripheral numbers of Treg cells may contribute to the development of MCTD-associated lung disease, whereas in SSc patients who had lung involvement, the reduce in peripheral number of Th17 cells may result in a severe imbalance of Th17/Treg cells, thereby promoting disease progression.

Fig 2.

Comparison of the levels of CD4+T lymphocyte subsets in patients who had pulmonary involvement and healthy controls: (A) There was no significant difference in the absolute number of Th1 cells in peripheral blood of different subjects; (B and C) The absolute number of peripheral Th2 cells and Th17 cells in patients with SSc were significantly reduced; (D and E) The ratio of Th17/Treg cells in PB of patients with MCTD were higher.*P< 0.05; **P< 0.01; ***P< 0.001.

References:

[1]Liu M, Wu W, Sun X, et al. New insights into CD4(+) T cell abnormalities in systemic sclerosis. Cytokine Growth Factor Rev. 2016 Apr; 28:31-6. doi: 10.1016/j.cytogfr.2015.12.002.

Acknowledgments:

None

Disclosure of Interests:

None declared

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival

BACKGROUND

The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.

RESULTS

In this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica 'Zhonghua 11', which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated seedling-lethal chlorosis 1 (slc1). The slc1 mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of OsSLC1 revealed that a single base (G) deletion was detected in the first exon of Os06g0710800 in the slc1 mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that OsSLC1 is responsible for the seedling-lethal chlorosis phenotype in the slc1 mutant. OsSLC1 was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of OsSLC1 affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of rps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.

CONCLUSION

We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the rps16 intron, and is essential for early chloroplast development and seedling survival in rice.

[Two cases of occupational frostbite]

The diagnosis, treatment, operation and diagnosis of two cases of occupational frostbite diagnosed in Shandong Academy of Occupational Healthy Occupational Medicine were analyzed retrospectively. In these two patients working in a low temperature environment, the finger frostbite did not arouse enough attention, one patient did not receive timely diagnosis and treatment, and one patient received timely medical treatment, but did not receive proper treatment, which ultimately led to the adverse consequences of finger amputation. The staff under the low temperature environment should strictly carry out the low temperature operation protection standard and improve their self-protection consciousness. If frostbite occurs, they should seek medical treatment in time, which can effectively reduce the disability rate.

Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

BACKGROUND

Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. CSSLs are also powerful tools for studying the effects of quantitative trait loci (QTLs) pyramiding and interaction on phenotypic variation.

RESULTS

Here, we developed three sets of CSSLs consisting of 81, 55, and 61 lines, which were derived from PA64s × 9311, Nipponbare × 9311 and PA64s × Nipponbare crosses, respectively. All of the 197 CSSLs were subjected to high-throughput genotyping by whole-genome resequencing to obtain accurate physical maps for the 3 sets of CSSLs. The 3 sets of CSSLs were used to analyze variation for 11 major agronomic traits in Hangzhou and Shenzhen and led to the detection of 71 QTLs with phenotypic effect that ranged from 7.6% to 44.8%. Eight QTLs were commonly detected under two environments for the same phenotype, and there were also 8 QTL clusters that were found. Combined with GWAS on grain length and expression profiles on young panicle tissues, qGL1 detected in CSSLs was fine mapped within a 119 kb region on chromosome 1 and LOC_Os01g53140 and LOC_Os01g53250 were the two most likely candidate genes.

CONCLUSIONS

Our results indicate that developing CSSLs genotyped by whole-genome resequencing are powerful tools for basic genetic research and provide a platform for the rational design of rice breeding. Meanwhile, the conjoint analysis of different CSSLs, natural population and expression profiles can facilitate QTL fine mapping.

Vaccine-Associated Maintenance of Epithelial Integrity Correlated With Protection Against Virus Entry

To identify the mechanisms by which human immunodeficiency virus type 1 (HIV-1) might penetrate the epithelial barrier during sexual transmission to women and the mechanisms of vaccine-associated protection against entry, we characterized early epithelial responses to vaginal inoculation of simian immunodeficiency virus strain mac251 (SIVmac251) in naive or SIVmac239Δnef-vaccinated rhesus macaques. Vaginal inoculation induced an early stress response in the cervicovaginal epithelium, which was associated with impaired epithelial integrity, damaged barrier function, and virus and bacterial translocation. In vaccinated animals, early stress responses were suppressed, and the maintenance of epithelial barrier integrity correlated with prevention of virus entry. These vaccine-protective effects were associated with a previously described mucosal system for locally producing and concentrating trimeric gp41 antibodies at the mucosal interface and with formation of SIV-specific immune complexes that block the stress responses via binding to the epithelial receptor FCGR2B and subsequent inhibitory signaling. Thus, blocking virus entry may be one protective mechanism by which locally concentrated non-neutralizing Ab might prevent HIV sexual transmission to women.