[The correlation between burst suppression on electroencephalogram during laparoscopic surgery and emergence delirium in elderly patients]

Objective: To investigate the relationship between intraoperative electroencephalogram burst suppression (BS) and emergence delirium (ED) in elderly patients undergoing elective laparoscopic surgery under total intravenous anesthesia (TIVA). Methods: From October 2017 to September 2019, a total of 358 elderly patients who underwent elective laparoscopic surgery under TIVA at Xiangya Hospital, Central South University, were included. Patients were divided into two groups based on the confusion assessment method for the intensive care unit (CAM-ICU) assessment conducted before leaving the post-anesthesia care unit (PACU): the ED group [n=63, 46 males, 17 females, average age of (70.8±0.6) years] and the non-ED group [n=295, 220 males, 75 females, average age of (69.7±0.2) years]. Preoperative general information, intraoperative conditions, and intraoperative electroencephalogram BS status were collected. A multivariate logistic regression model was employed to identify risk factors associated with ED. Results: In the ED group, the duration of surgery, intraoperative blood loss, the burst suppression ratio (BSR)>10% lasting for more than 1 minute were (224.4±9.6) min, (240.8±33.9) ml, 36.5% (23/63), respectively, which were higher than those of the non-ED group [(204.7±3.6) min, (150.5±9.2) ml, 21.7% (64/295), all P<0.05]. Multivariate logistic regression analysis revealed that a longer duration of education was a protective factor for ED (OR=0.904, 95%CI: 0.833-0.982,P=0.016), whereas increased intraoperative blood loss (OR=1.002, 95%CI: 1.000-1.003, P=0.013) and BSR>10% lasting for more than 1 minute (OR=2.131, 95%CI: 1.004-4.524,P=0.049) were identified as risk factors for ED. Conclusion: In elderly patients undergoing laparoscopic surgery under TIVA, intraoperative electroencephalogram BS may be a risk factor for ED.

A syntelog-based pan-genome provides insights into rice domestication and de-domestication

BACKGROUND

Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.

RESULTS

Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.

CONCLUSIONS

This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation.

PlantcircBase 7.0: Full-length transcripts and conservation of plant circRNAs

Circular RNA (circRNA) is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants. Five years ago, we developed a comprehensive plant circRNA database (PlantcircBase), which has attracted much attention from the plant circRNA community. Here, we report an updated PlantcircBase (v.7.0), which contains 171,118 circRNAs from 21 plant species. Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing (RNA-seq) datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study. A plant multiple conservation score (PMCS), based on the conservation of both sequence and expression profiles, was calculated for each circRNA to quantify and compare the conservation of all circRNAs. A new parameter, plant circRNA confidence level (PCCL), is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA. All this information and other details of circRNAs can be browsed, searched, and downloaded from PlantcircBase 7.0, which also provides online bioinformatics tools for visualization and sequence alignment. PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.

[Analysis of differences and influencing factors of liver injury associated with different strains of 2019-nCoV infection]

Objective: To analyze whether there are differences and related influencing factors in liver injury associated with different strains of 2019-nCoV/SARS-CoV-2 infection. Methods: Data of epidemiology, clinical symptoms, laboratory tests, and treatment outcomes of patients with COVID-19 infection confirmed with Alpha and Delta virus strain in Zhejiang Province were retrospectively collected. Statistical analysis was performed using independent samples t-test or Mann-Whitney U test, χ² test or Fisher's exact test, and logistic regression analysis. Results: A total of 788 and 381 cases with Alpha and Delta virus strain were included. Vaccination ratio was 0% in Alpha and 85.30% in Delta group (P<0.001), The proportion of patients with fever (80.71% vs. 40.94%, P<0.001) was significantly higher in Alpha than Delta strain group. The proportion of critical ill patients was significantly higher in Delta group (9.90% vs. 1.57%, respectively, P<0.001). The virus negative conversion time was significantly longer in Delta than Alpha group (22 d vs. 11 d, P<0.001), but the incidence of liver injury was significantly higher in Alpha than Delta group (20.05% vs. 13.91%, P=0.011). Univariate analysis showed that Alpha virus strain infection, male sex, body mass index, chronic liver disease, fever, diarrhea, shortness of breath, severe/critical illness, elevated creatine kinase (CK), elevated international normalized ratio (INR) and an elevated neutrophil/lymphocyte ratio was significantly associated with an increased risk of liver injury occurrence, and in patients with pharyngeal pain the risk of liver injury occurrence was significantly reduced. Multivariate analysis showed that shortness of breath [OR, 2.667 (CI: 1.389-5.122); P=0.003], increased CK [OR, 2.544 (CI: 1.414-4.576); P=0.002] and increased INR [OR, 1.721] (CI: 1.074-2.758); P=0.024] was significantly associated with an increased risk of liver injury occurrence, and in patients with pharyngeal pain the risk of liver injury occurrence was significantly reduced [OR, 0.424 (CI: 0.254-0.709); P=0.001]. Conclusion: Although the virulence of the Delta is stronger than Alpha strain, most patients infected with Delta strain vaccinated against COVID-19 in Zhejiang province had milder clinical symptoms and a lower incidence and degree of liver injury. Notably, the infection risk even remains after vaccination; however, symptoms and the incidence of severe and critical illness can be significantly reduced.

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants

Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

Genomic insights into the evolution of Echinochloa species as weed and orphan crop

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Recent origination of circular RNAs in plants

Circular RNA (circRNA) is a kind of new regulatory RNA with diverse biological functions. Numerous circRNAs have been identified in many plant species; however, evolution of plant circRNAs remains largely unknown. In this study, we assembled full-length sequences of 6519 rice (Oryza sativa) circRNAs and analyzed their conservation in another 46 plant species based on comparison of sequences and expression patterns. We found that, at the genomic level, 8.7% of the 6519 circRNAs were conserved in dicotyledonous plants and 49.1% in Oryza genus. Meanwhile, 57.8% of parental protein-coding genes of the rice circRNAs originated recently after divergence of monocotyledonous plants, implying recent origin of the majority of rice circRNAs, a conclusion further supported by the results based on analysis of 4663 full-length circRNAs in Arabidopsis thaliana. Accordingly, we proposed three models to address the origination of different types of circRNAs. Taken together, the results obtained in this study provide new insights for the evolutionary dynamics of plant circRNAs and candidate circRNAs for further functional exploration.

The complete chloroplast genome of Echinochloa haploclada

The genus Echinochloa (Poaceae) includes orphan crops and important agricultural weeds. Here, we assembled the complete chloroplast genome of a diploid Echinochloa species (E. haploclada). The chloroplast genome is 139,844 bp in length, which includes a large single copy region (81,893 bp), a small single copy region (12,533 bp) and two separated inverted repeat regions (45,418 bp). A total of 119 unique genes were annotated, consisting of 83 protein-coding genes, 32 tRNA genes and 4 rRNA genes. Hexaploid E. crus-galli, one of the most serious weeds worldwide, was derived from a hybrid between tetraploid E. oryzicola and an unknown diploid species. Based on chloroplast genomes of eight Echinochloa species (varieties), the phylogenetic analysis showed that E. crus-galli clustered firstly with diploid E. haploclada rather than tetraploid E. oryzicola, supporting previous assumption that E. oryzicola is the paternal donor of E. crus-galli.

Orphan Crops and their Wild Relatives in the Genomic Era

More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.

The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. In this study, we generated and analyzed high-quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola), and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.

RiceRelativesGD: a genomic database of rice relatives for rice research

Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208 321 specific genes and 13 643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.

[Relationship between liver controlled attenuation parameters and body fat mass and its distribution]

Objective: To explore the relationship between liver controlled attenuation parameters (CAP) and body fat mass and its distribution. Methods: From May to December 2018, 978 adult patients visited at the fatty liver center of the Third People's Hospital of Changzhou were treated. The patient's liver controlled attenuation parameters were measured by transient elastography and the body fat mass and its distribution were measured by bioelectrical impedance technology. Pearson's correlation coefficient was adopted to describe the correlation between liver CAP value and body mass index (BMI), body fat mass index (BFMI), trunk fat mass index (TFMI), limbs fat mass index (LFMI) and visceral fat area (VFA). Receiver operating characteristic curve (ROC) and area under the curve (AUC) were used to evaluate BMI, BFMI, TFMI, LFMI and VFA to differentiate the cut-off points and efficacy of CAP for diagnosing grading of fatty liver changes in S0-1 and S2-3. Results: In 653 cases of male, S0 ~ S3 accounted for 4.90%, 3.37%, 22.36% and 69.37%, respectively, and in 325 cases of females, S0 ~ S3 accounted for 7.38%, 6.46%, 13.23% and 72.92%, respectively. Female patients had more visceral, trunk and limbs fat than male (P < 0.01). Body mass, body fat mass, body fat percentage, BMI, BFMI, TFMI, LFMI, and VFA were increased in male and female patients with increasing liver fat grade (P < 0.01). CAP values ​​of male and female patients were positively correlated with BMI, BFMI, TFMI, LFMI and VFA. Percentage of body fat mass increased with increasing liver fat grade (male: F = 13.42, P < 0.001; female: F = 3.22, P = 0.023); while limb fat mass percentage did not increase with liver fat grade (Male: F = 1.13, P = 0.34; female: F = 1.05, P = 0.37). Hepatic steatosis grading (S0 ~ 1 or S2 ~ 3) diagnosed with CAP were distinguished through BMI, BFMI, TFMI, LFMI and VFA. AUC was 0.80 ~ 0.82 in males (P < 0.01), and 0.75 ~ 0.78 in females (P < 0.01). Conclusion: The liver CAP value is positively correlated with the body's limbs, trunk and visceral fat, and has a strong correlation with trunk and visceral fat. BMI, BFMI, TFMI, LFMI and VFA up to some extent can identify the CAP diagnosis of grading of fatty liver changes in S0-1 and S2-3.

Genomic evidence of human selection on Vavilovian mimicry

Vavilovian mimicry is an evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans. Unravelling its molecular mechanisms will extend our knowledge of mimicry and contribute to our understanding of the origin and evolution of agricultural weeds, an important component of crop biology. To this end, we compared mimetic and non-mimetic populations of Echinochloa crus-galli from the Yangtze River basin phenotypically and by genome resequencing, and we show that this weed in rice paddies has evolved a small tiller angle, allowing it to phenocopy cultivated rice at the seedling stage. We demonstrate that mimetic lines evolved from the non-mimetic population as recently as 1,000 yr ago and were subject to a genetic bottleneck, and that genomic regions containing 87 putative plant architecture-related genes (including LAZY1, a key gene controlling plant tiller angle) were under selection during the mimicry process. Our data provide genome-level evidence for the action of human selection on Vavilovian mimicry.

Characteristics of plant circular RNAs

Circular RNA (circRNA) is a kind of covalently closed single-stranded RNA molecules that have been proved to play important roles in transcriptional regulation of genes in diverse species. With the rapid development of bioinformatics tools, a huge number (95143) of circRNAs have been identified from different plant species, providing an opportunity for uncovering the overall characteristics of plant circRNAs. Here, based on publicly available circRNAs, we comprehensively analyzed characteristics of plant circRNAs with the help of various bioinformatics tools as well as in-house scripts and workflows, including the percentage of coding genes generating circRNAs, the frequency of alternative splicing events of circRNAs, the non-canonical splicing signals of circRNAs and the networks involving circRNAs, miRNAs and mRNAs. All this information has been integrated into an upgraded online database, PlantcircBase 3.0 (http://ibi.zju.edu.cn/plantcircbase/). In this database, we provided browse, search and visualization tools as well as a web-based blast tool, BLASTcirc, for prediction of circRNAs from query sequences based on searching against plant genomes and transcriptomes.

Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared with its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study we analyzed the transcriptomes of Brassica napus parental lines and their F₁ hybrids at three stages of early flower development. Phenotypically, the F₁ hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormone (auxin and salicylic acid) response genes are significantly altered in the F₁ hybrids relative to the parental lines. We also found evidence for decreased expression divergence of the homoeologous gene pairs in the allopolyploid F₁ hybrids and suggest that high-parental expression-level dominance plays an important role in heterosis. Small RNA and methylation studies aimed at examining the epigenetic effect of the changes in gene expression level in the F₁ hybrids showed that the majority of the small interfering RNA (siRNA) clusters had a higher expression level in the F₁ hybrids than in the parents, and that there was an increase in genome-wide DNA methylation in the F₁ hybrid. Transposable elements associated with siRNA clusters had a higher level of methylation and a lower expression level in the F₁ hybrid, implying that the non-additively expressed siRNA clusters resulted in lower activity of the transposable elements through DNA methylation in the hybrid. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms contribute to heterosis during early flower development in allopolyploid B. napus.

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.

Widespread noncoding circular RNAs in plants

A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.

A host plant genome (Zizania latifolia) after a century-long endophyte infection

Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop 'Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.

A host plant genome (Zizania latifolia) after a century-long endophyte infection

Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop 'Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.

Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticated indica and japonica rice. Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide. While its formation is poorly understood, massive amounts of rice genomic data may provide new insights into this issue. In this study, we determined genomes of three weedy rice samples from the lower Yangtze region, China, and investigated their phylogenetics, population structure and chromosomal admixture patterns. The phylogenetic tree and principle component analysis based on 46,005 SNPs with 126 other Oryza accessions suggested that the three weedy rice accessions were intermediate between japonica and indica rice. An ancestry inference study further demonstrated that weedy rice had two dominant genomic components (temperate japonica and indica). This strongly suggests that weedy rice originated from indica-japonica hybridization. Furthermore, 22,443 novel fixed single nucleotide polymorphisms were detected in the weedy genomes and could have been generated after indica-japonica hybridization for environmental adaptation.

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19-0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis.

Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress

Background

DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.

Results

In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in Populus drought stress responses through the changes of DNA methylation.

Conclusions

These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.

A diverse set of miRNAs responsive to begomovirus-associated betasatellite in Nicotiana benthamiana

BACKGROUND

Roles of microRNAs (miRNAs) and short interfering RNAs (siRNAs) in biotic stress responses, e.g., viral infection, have been demonstrated in plants by many studies. Tomato yellow leaf curl China virus (TYLCCNV) is a monopartite begomovirus that can systemically infect Solanaceae plants, and induces leaf curling, yellowing and enation symptoms when co-inoculated with a betasatellite (TYLCCNB). The released genome sequence of Nicotiana benthamiana provides an opportunity to identify miRNAs and siRNAs responsive to begomovirus-associated betasatellite in N. benthamiana.

RESULTS

miRNAs were identified in three small RNA libraries generated using RNA isolated from N. benthamiana plants systemically infected with TYLCCNV (Y10A) alone, co-infected with Y10A and its betasatellite TYLCCNB (Y10β) or a TYLCCNB mutant (Y10mβ) that contains a mutated βC1, the sole betasatellite-encoded protein. A total of 196 conserved miRNAs from 38 families and 197 novel miRNAs from 160 families were identified. Northern blot analysis confirmed that expression of species-specific miRNAs was much lower than that of conserved miRNAs. Several conserved and novel miRNAs were found to be responsive to co-infection of Y10A and Y10β but not to co-infection of Y10A and Y10mβ, suggesting that these miRNAs might play a role unique to interaction between Y10β and N. benthamiana. Additionally, we identified miRNAs that can trigger the production of phased secondary siRNAs (phasiRNAs).

CONCLUSIONS

Identification of miRNAs with differential expression profiles in N. benthamiana co-infected with Y10A and Y10β and co-infected with Y10A and Y10mβ indicates that these miRNAs are betasatellite-responsive. Our result also suggested a potential role of miRNA-mediated production of phasiRNAs in interaction between begomovirus and N. benthamiana.

Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean

A wide range of RNA species interacting with microRNAs (miRNAs) form a complex gene regulation network and play vital roles in diverse biological processes. In this study, we performed a genome-wide identification of endogenous target mimics (eTMs) for miRNAs and phased-siRNA-producing loci (PHAS) in soybean with a focus on those involved in lipid metabolism. The results showed that a large number of eTMs and PHAS genes could be found in soybean. Additionally, we found that lipid metabolism related genes were potentially regulated by 28 miRNAs, and nine of them were potentially further regulated by a number of eTMs with expression evidence. Thirty-three miRNAs were found to trigger production of phasiRNAs from 49 PHAS genes, which were able to target lipid metabolism related genes. Degradome data supported miRNA- and/or phasiRNA-mediated cleavage of genes involved in lipid metabolism. Most eTMs for miRNAs involved in lipid metabolism and phasiRNAs targeting lipid metabolism related genes showed a tissue-specific expression pattern. Our bioinformatical evidences suggested that lipid metabolism in soybean is potentially regulated by a complex non-coding network, including miRNAs, eTMs, and phasiRNAs, and the results extended our knowledge on functions of non-coding RNAs.

De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa

Background

Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as −30°C during the winter. Although A. mongolicus is an ideal model to study the plant response to cold stress, insufficient genomic resources for this species are available in public databases. To identify genes involved in cold acclimation (a phenomenon experienced by plants after low temperature stress), a high-throughput sequencing technology was applied.

Results

We sequenced cold-treated and control (untreated) samples of A. mongolicus, and obtained 65,075,656 and 67,287,120 high quality reads, respectively. After de novo assembly and quantitative assessment, 82795 all-unigenes were finally generated with an average length of 816 bp. We then obtained functional annotations by aligning all-unigenes with public protein databases including NR, SwissProt, KEGG and COG. Differentially expressed genes (DEGs) were investigated using the RPKM method. Overall, 9309 up-regulated genes and 23419 down-regulated genes were identified. To increase our understanding of these DEGs, we performed GO enrichment and metabolic pathway enrichment analyses. Based on these results, a series of candidate genes involved in cold responsive pathways were selected and discussed. Moreover, we analyzed transcription factors, and found 720 of them are differentially expressed. Finally, 20 of the candidate genes that were up-regulated and known to be associated with cold stress were examined using qRT-PCR.

Conclusions

In this study, we identified a large set of cDNA unigenes from A. mongolicus. This is the first transcriptome sequencing of this non-model species under cold-acclimation using Illumina/Solexa, a next-generation sequencing technology. We sequenced cold-treated and control (untreated) samples of A. mongolicus and obtained large numbers of unigenes annotated to public databases. Studies of differentially expressed genes involved in cold-related metabolic pathways and transcription factors facilitate the discovery of cold-resistance genes.

Evolutionary analyses of non-family genes in plants

There are a large number of 'non-family' (NF) genes that do not cluster into families with three or more members per genome. While gene families have been extensively studied, a systematic analysis of NF genes has not been reported. We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94,000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae wide, angiosperm specific, monocot specific, dicot specific, and those that were species specific. Our analysis revealed that the NF genes resulted largely from less frequent gene duplications and/or a higher rate of gene loss after segmental duplication relative to genes in both low-copy-number families (LF; 3-10 copies per genome) and high-copy-number families (HF; >10 copies). Furthermore, we identified functions enriched in the NF gene set as compared with the HF genes. We found that NF genes were involved in essential biological processes shared by all plant lineages (e.g. photosynthesis and translation), as well as gene regulation and stress responses associated with phylogenetic diversification. In particular, our analysis of an Arabidopsis protein-protein interaction network revealed that hub proteins with the top 10% most connections were over-represented in the NF set relative to the HF set. This research highlights the roles that NF genes may play in evolutionary and functional genomics research.

Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics

Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of biofuels from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidence supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional characterization in relation to cell wall biosynthesis.

Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis

Glycosyltransferase family14 (GT14) belongs to the glycosyltransferase (GT) superfamily that plays important roles in the biosynthesis of cell walls, the most abundant source of cellulosic biomass for bioethanol production. It has been hypothesized that DUF266 proteins are a new class of GTs related to GT14. In this study, we identified 62 GT14 and 106 DUF266 genes (named GT14-like herein) in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Our phylogenetic analysis separated GT14 and GT14-like genes into two distinct clades, which were further divided into eight and five groups, respectively. Similarities in protein domain, 3D structure and gene expression were uncovered between the two phylogenetic clades, supporting the hypothesis that GT14 and GT14-like genes belong to one family. Therefore, we proposed a new family name, GT14/GT14-like family that combines both subfamilies. Variation in gene expression and protein subcellular localization within the GT14-like subfamily were greater than those within the GT14 subfamily. One-half of the Arabidopsis and Populus GT14/GT14-like genes were found to be preferentially expressed in stem/xylem, indicating that they are likely involved in cell wall biosynthesis. This study provided new insights into the evolution and functional diversification of the GT14/GT14-like family genes.

Molecular characterization of putative vacuolar NHX-type Na(+)/H(+) exchanger genes from the salt-resistant tree Populus euphratica

The vacuolar NHX-type Na(+)/H(+) exchangers play a key role in salt tolerance in plants. However, little is known about the Na(+)/H(+) exchangers in the salt-resistant tree, Populus euphratica. In this study, we identified six putative vacuolar Na(+)/H(+) exchanger genes from P. euphratica, designated as PeNHX1-6. Real-time polymerase chain reaction indicated that the PeNHX1/3/6 transcripts were abundant compared with the other three PeNHX genes in the three tissues (roots, stems and leaves) examined. After NaCl treatment for 6 h, the transcript levels of PeNHX1-6 were upregulated in the roots. To address the function of PeNHX1-6, complementation studies were performed with the salt-sensitive yeast mutant strain R100, which lacks activity of the endosomal Na(+)/H(+) antiporter NHX1. The results showed that PeNHX1-6 compensates, at least in part, for the function of yeast NHX1. Moreover, PeNHX3 was targeted to the tonoplast when transiently expressed in onion. Together, these results suggest that PeNHX1-6 function as vacuolar Na(+)/H(+) exchangers and that PeNHX products play an important role in the salt resistance of P. euphratica.

Fast optical switching via stimulated Raman adiabatic passage

We demonstrate a new approach to fast optical switching with a technique based on stimulated Raman adiabatic passage in which a laser pulse switches the probe field on and off via another coupling pulse. This new kind of optical switching is not limited by the decay rate of an excited state and can operate in the subnanosecond time domain. The experimental observation in Rb atomic vapor is in good agreement with numerical simulations.

[Clinical application of the medial multiplex flap pedicled with the posterior tibial vessel]

OBJECTIVE

To investigate the clinical results of the medial multiplex flap pedicled with the posterior tibial vessel.

METHODS

Twelve cases with soft tissue defects and bone defects of limbs were treated with the medial multiplex flap pedicled with the posterior tibial vessel from September 1992 to May 1999. Among them, bone and soft tissue defects following opened fracture in 7 cases, chronic ulcer following chronic osteomyelitis in 2 cases, melanoepithelioma in 2 cases, bone and soft tissue defects following osteoma resection in 1 case. The bone defect area was from 2.5 cm x 5.0 cm to 4.5 cm x 11.0 cm. Free graft was performed in 5 cases, bridged transposition in 3 cases and reversal transposition in 4 cases, among them, periosteal myocutaneous flap with autogenous or allogeneic bone grafting in 8 cases, myocutaneous flap in 4 cases. The area of the flaps from 6 cm x 8 cm to 12 cm x 25 cm.

RESULTS

All flaps were healed by first intention, but in the distal fragments of bigger flaps were partially necrosed in 2 cases. In 10 cases bone healing were obtained after 16 weeks of operation according to the X-ray photos. All cases were followed up from 6 to 18 months. All cases achieved satisfactory result but 1 case died because of lung metastasis of osteoma.

CONCLUSION

The multiplex graft pedicled with the posterior tibial vessel is an ideal graft for repairing the large soft tissue defects and bone defects, because it has such advantages as adequate blood supply, big vascular diameter, long pedicle and big dermatomic area.

[Clinical study of 76 cases of counterattack induced by acute organic phosphorus pesticides intoxication]

76 cases of counterattack induced by acute organic phosphorus pesticides intoxication were analysed. The activity of cholinesterase did not show a significant difference before the counterattack as compared to that after the counterattack (P > 0.05). The average dosage of atropine for pre-atropinization was 58.6 +/- 2.7 mg/h and it was 203.9 +/- 17.7 mg/h between the post-counterattack and the second atropinization (P < 0.01). Compared the mortality in reaching and non-reaching the second atropinization was 22.8% VS 100% (P < 0.01). The survival rate was 37.5% in collaborating blood transfusion cases and 20.6% in noncollaborating ones (P > 0.05). We also studied on the treatment, mechanism, precursory symptoms, causes of death, degrees of intoxication and pesticide types etc.

[Prognosis of severe organic phosphorus pesticide intoxication and the effect of atropine treatment: analysis of 506 cases]

The results of atropine treatment in 506 cases of severe organic phosphorus pesticide intoxication are reported. Among the variables which might effect the results of treatment, the average dosage of atropine was related intimately to the prognosis (standard coefficient of regression bi = 0.4702, P less than 0.01). When the average drug dosage was 40-80 ng/h, the mortality was 26.6% and much lower than other groups (P less than 0.01). Intravenous administration given at regular intervals was better than continuous drip; the mortality dropped to 61.2% from 90.9% (P less than 0.01). Both inadequate atropinization and atropine intoxication were less frequently seen during intermitten injection (P less than 0.01).

[Determination of ethyl paraben in shengmaiyin oral liquid using gas chromatography]

This paper describes a gas chromatographic method for the determination of preservative--ethyl paraben in shengmaiyin Oral Liquid. The method is simple, rapid and accurate. The recovery is good (99.5%), and the coefficient of variation is 0.288%.

[Irreversible action of the opioid agonist alpha-CAM and its reaction with SH groups at opioid receptor binding sites]

7 alpha-Bis (beta-chloroethyl)amino-methyl-6,14-endoethenotetrahydrooripavine (alpha-CAM) was found to bind to opioid receptors irreversibly and react directly with sulfhydryl (SH) groups in P2 preparations of rat brain. The P2 preparations were pretreated as follows: protection of the SH groups at the opioid receptor binding sites by morphine or etorphine, and inactivation of the SH groups outside the binding sites by N-ethylmaleimide (NEM), followed by removal of the morphine or etorphine by washing. alpha-CAM was still able to bind the pretreated P2 preparations in an irreversible manner. The results indicate that the formation of covalent bonds between alpha-CAM and the SH groups of opioid receptor binding sites is possibly one of the biochemical mechanisms of the irreversible action of alpha-CAM.

The biphasic effects of some opiates and opioid peptides on the rat vas deferens

It has been found that the effects of opiates and opioid peptides on RVD are of two types. Compounds of the first type such as Etor, Eton, fentanyl and prodine derivatives, Met- and Leu-Enk and DADL are biphasic in nature. At lower concentrations (10(-8)-10(-5) M) they have inhibitory effects and at higher concentrations (10(-5)-10(-4) M) they are excitatory. Compounds of the second type, such as Mor, benzomorphan derivates, Cyc and SKF and the antagonist Nx have virtually no or only weakly inhibitory effects but may antagonize the inhibitory effect produced by the first group of compounds at lower concentrations. MC belongs to the second type, but it cannot antagonize the inhibitory effect of beta-End. The results are discussed in terms of multiple receptors, the high and low affinity binding sites, and the interrelationship between receptors.