The Pharus latifolius genome bridges the gap of early grass evolution.

The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a grass species (producing a true spikelet) in the subfamily Pharoideae, a sister lineage to the core Poaceae including the (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) and Bambusoideae, Oryzoideae, and Pooideae (BOP) clades. Our results indicate that the P. latifolius genome has evolved slowly relative to cereal grass genomes, as reflected by moderate rates of molecular evolution, limited chromosome rearrangements and a low rate of gene loss for duplicated genes. We show that the ρ-WGD event occurred approximately 98.2 million years ago (Ma) in a common ancestor of the Pharoideae and the PACMAD and BOP grasses. This was followed by contrasting patterns of diploidization in the Pharus and core Poaceae lineages. The presence of two FRIZZY PANICLE-like genes in P. latifolius, and duplicated MADS-box genes, support the hypothesis that the ρ-WGD may have played a role in the origin and functional diversification of the spikelet, an adaptation in grasses related directly to cereal yields. The P. latifolius genome sheds light on the origin and early evolution of grasses underpinning the biology and breeding of cereals.

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence.].

PEG modification enhances the in vivo stability of bioactive proteins immobilized on magnetic nanoparticles.

OBJECTIVE: To increase the in vivo stability of bioactive proteins via optimized loading methods. RESULTS: ß-Glucosidase (ß-Glu), as a model protein, was immobilized on magnetic nanoparticles(denoted as MNP-ß-Glu) by chemical coupling methods and was further modified by poly(ethylene glycol) (PEG) molecules (denoted as MNP-ß-Glu-PEG) to increase its stability. The physicochemical properties of the as-prepared nanohybrids, including the particle size, zeta potential, and enzyme activity, were well characterized. The proper MNP/ß-Glu feed ratio was important for optimizing the particle size. Analysis of enzyme activity showed that the stability of immobilized ß-Glu compared with free ß-Glu was lower in deionized water and higher in blood serum at 37 °C. MNP-ß-Glu-PEG retained 77.9% of the initial activity within 30 days at 4 °C, whereas the free enzyme retained only 58.2%. Pharmacokinetic studies of Sprague-Dawley (SD) rats showed that the MNP-ß-Glu-PEG group retained a higher enzyme activity in vivo (41.46% after 50 min) than the MNP-ß-Glu group (0.03% after 50 min) and the ß-Glu group (0.37% after 50 min). Moreover, in contrast to the MNP-ß-Glu group, the enzyme activity was not fully synchronous with the decrease in the Fe concentration in the MNP-ß-Glu-PEG group. CONCLUSIONS: All findings indicated that the method of immobilization on magnetic nanoparticles and PEG modification is promising for the application of bioactive proteins in vivo.

Induction of apoptosis and autophagy by calcifying nanoparticles in human bladder cancer cells.

Calcifying nanoparticles have been linked to various types of human disease, but how they contribute to disease processes is unclear. Here, we examined whether and how calcifying nanoparticles isolated from patients with kidney stones are cytotoxic to human bladder cancer cells. Calcifying nanoparticles were isolated from midstream urine of patients with renal calcium oxalate stones and examined by electron microscopy. Human bladder cancer cells (EJ cells) were cultured in the presence of calcifying nanoparticles or nanohydroxyapatites for 12 and 72 h and examined for toxicity using the Cell Counting Kit-8, for autophagy using transmission electron microscopy and confocal microscopy, and for apoptosis using fluorescence microscopy, transmission electron microscopy, and flow cytometry. Changes in protein expression were analyzed by Western blotting. The results showed that the size and shape of the isolated calcifying nanoparticles were as expected. Calcifying nanoparticles were cytotoxic to EJ cells, more so than nanohydroxyapatites, and this was due, at least in part, to the production of intracellular reactive oxygen species. Transmission electron microscopy showed that calcifying nanoparticles were packaged into vesicles and autolysosomes. Calcifying nanoparticles induced greater autophagy and apoptosis than nanohydroxyapatites. Our findings demonstrate that calcifying nanoparticles can trigger bladder cancer cell injury by boosting reactive oxygen species production and stimulating autophagy and apoptosis.

Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

[Factors influencing the postoperative resolution of varicocele-associated scrotal pain].

OBJECTIVE: To investigate the factors influencing the postoperative resolution of varicocele-associated scrotal pain. METHODS: Using the keywords "varicocele", "testicular pain", "scrotal pain", "painful varicocele", "ligation", and "varicocelectomy", we searched the PubMed, Embase, Cochrane Collaboration's Database, CNKI, Wanfang, and VIP Database up to October 2016 for the studies relating to surgical treatment of varicocele-associated scrotal pain. We assessed the quality of the cohort studies included using the Newcastle-Ottawa Scale and that of the randomized controlled trials included with the Cochrane Collaboration's tool. We conducted a meta-analysis using the RevMan software. RESULTS: Finally 14 studies were included in this meta-analysis, of which, 2 involved the history of disease, 8 involved the nature of pain, 2 involved the intensity of pain, 9 involved the grade of varicocele, 3 involved the side of varicocele, 9 involved surgical approaches, 3 involved surgical techniques, and 4 involved postoperative recurrence. The pain resolution rate was significantly higher after subinguinal ligation than after high or inguinal ligation (RR = 0.82, 95% CI: 0.76－0.89, P <0.01; RR = 0.92, 95% CI: 0.86－0.99, P = 0.02), and so was it after microsurgery than after laparoscopic varicocelectomy (RR = 0.77, 95% CI: 0.60－0.99, P = 0.04). CONCLUSIONS: Subinguinal varicocelectomy and microsurgery are more effective options than laparoscopic and high or trans-inguinal ligation of the spermatic vein for resolution of varicocele-associated scrotal pain, while the history of disease, the nature and intensity of pain, the grade and side of varicocele, or postoperative recurrence cannot be regarded as the influencing factors.

Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.

Systematic proteomics analysis revealed different expression of laminin interaction proteins in breast cancer: lower in luminal subtype and higher in claudin-low subtype.

Background: Breast cancer is a major public health concern. Proteomics enables identification of proteins with aberrant properties. Here, we identified proteins with abnormal expression levels in breast cancer tissues and systematically analyzed and validated the data to locate potential diagnostic and therapeutic targets. Methods: Protein expression level in breast cancer tissues and para-carcinoma tissues were detected by Isobaric Tags for Relative and Absolute Quantification (iTRAQ) technology and further screened through Gene Expression Profiling Interactive Analysis (GEPIA) database. Cellular components, protein domain and Reactome pathway analysis were performed to screen functional targets. Abnormal expression levels of functional targets were validated by Oncomine database, quantitative real time polymerase chain reaction (qRT-PCR) and proteomics detection. Protein correlation analysis was performed to explain the abnormal expression levels of potential targets in breast cancer. Results: Overall, 207 and 207 proteins were up- and down-regulated, respectively, in breast cancer tissues, and approximately 50% were also detected in the GEPIA database. The overlapping proteins were mainly extracellular proteins containing epidermal growth factor-like domain in leukocyte adhesion molecule (EGF-Lam) domain and enriched in laminin interaction pathway. Moreover, the downregulated laminin interaction proteins could be functional targets, which were also validated through Oncomine-Richardson and Oncomine-Curtis database. However, the lower expression level of laminin interaction proteins only fit for luminal breast cancer cells with no or low metastasis ability because the proteins achieved higher expression level in more invasive claudin-low breast cancer cells. In addition, when compared with corresponding in situ carcinoma tissues, above-mentioned proteins also showed higher expression levels in invasive carcinoma tissues. Finally, we have revealed the negative correlation between the laminin interaction proteins and the claudins. Conclusions: The laminin interaction protein, especially for laminins with ß1 and γ1 subunits and their integrin receptors with α1 and α6 subunits, showed lower expression levels in luminal breast cancer with no or lower metastatic ability, but showed higher expression levels in claudin-low breast cancer with higher metastatic ability; and their higher expression could be related to the low claudin expression.

Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

Research progress on the molecular mechanism of electroacupuncture at "Zusanli" (ST36) for regulating gastrointestinal dysfunction. / 电针"足三里"è°ƒèŠ‚èƒƒè‚ åŠŸèƒ½å¼‚å¸¸çš„åˆ†å­æœºåˆ¶ç ”ç©¶è¿›å±•.

Gastrointestinal dysfunction is manifested as digestive symptoms. Clinically, Zusanli (ST36) is crucial in the acupoint prescriptions of acupuncture no matter which type of the disease is differentiated in traditional Chinese medicine, but the underlying mechanism remains to be explored. Aiming to summarize the current status of the researches in terms of ameliorating gastrointestinal mucosal damage and regulating gastrointestinal motility disorders, we systematically reviewed the basic researches on the intervention with electroacupuncture (EA) at "ST36" in treatment of the diseases related to gastrointestinal dysfunction in the past 5 years, after searching the articles from Chinese and English databases. The results suggest that EA at ST36 may regulate the local gastrointestinal inflammation, oxidative stress and immune microenvironment to relieve gastrointestinal mucosal damage and adjust gastrointestinal motility disorders by means of modulating the central and peripheral nerve signaling as well as the function of mast cells and Cajal interstitial cells.

Five new and noteworthy species of Epidendroideae (Orchidaceae) from southwestern China based on morphological and phylogenetic evidence.

Five new orchid species from southwestern China's Yunnan Province and the Tibetan Autonomous Region, Neottialihengiae, Neottiachawalongensis, Papilionanthemotuoensis, Gastrochiluslihengiae, and Gastrochilusbernhardtianus, are described and illustrated. To confirm their identities, and to resolve phylogenetic relationships, we sequenced the complete plastomes of these taxa with their congeneric species, adding new plastomes of three Neottia species, two Papilionanthe species and nine Gastrochilus species. Combined with published plastid sequences, our well-resolved phylogeny supported the alliance of N.lihengiae with the the N.grandiflora + N.pinetorum clade. Neottiachawalongensis is now sister to N.alternifolia, while P.motuoensis is closely related to P.subulata + P.teres. Conversely, phylogenetic analyses based on complete plastomes and plastid sequences showed inconsistent relationships among taxa in the genus Gastrochilus, but the two new species, G.lihengiae and G.bernhardtianus were supported by all datasets.

[Studies on fluorescence properties of a novel acylhydrazone ligands and its Sn metal complexes].

The molecular structure and spectral properties of a novel acylhydrazone ligands 2-hydroxy-naphthaldehyde-5-chloro-salicyloylhydrazone (H3L) and its Sn metal complexes [(n-Bu2)Sn(HL)] in solution, crystal and thin films were investigated by using steady state and time resolved fluorescence spectrum. The experimental results show that for H3L, compared with it in solution, the fluorescence intensity is enhanced as it is crystal and thin films, the fluorescence peak is red-shift, and the excited state lifetime is longer. The transition energies of the unimolecule is 240.2 kJ x mol(-1). For (n-Bu2)Sn(HL), the fluorescence intensity is stronger as it is crystal than it is in solution and the fluorescence peak is red-shilft, the excited state lifetime is longer. The fluorescence is quenched as it is in thin films. The transition energies of the unimolecule is 230.4 kJ x mol(-1). The fluorescence intensity of (n-Bu2)Sn(HL) is four times higher than the H3L. The excited state lifetime of (n-Bu2) Sn(HL) is longer than H2L too. In theory, these phenomena could be explained by that with the increase of the conjugated system and the rigid construction, the fluorescence intensity is stronger and the excited state lifetime is longer.

Clinical analysis of 60 children with pelvic fracture and associated injuries: an observational study.

BACKGROUND: The injury mechanism of a pelvic fracture is primarily high-energy injury, and it is easily combined with injuries to other tissues and organs. This study aimed to investigate the clinical effectiveness of early diagnosis and treatment of pelvic fractures and associated injuries in children. METHODS: The diagnosis and treatment of 60 children with pelvic fractures and associated injuries who were admitted to our hospital from January 2005 to December 2016 were retrospectively analyzed. Among these patients, 36 were male, and 24 were female. The patients' ages ranged within 2-15 years, with an average of 7.6 years old. The pelvic fractures were classified based on the Torode and Zieg classification; among the patients, 12 had type I, 16 had type II, 20 had type III, and 12 had type IV. All patients received early diagnosis, immediate anti-shock measures, aggressive treatment of associated injuries, and early reduction and fixation of the pelvic fractures after admission. RESULTS: Of the 60 patients, 28 had injuries caused by traffic accidents, 26 had injuries caused by falling from high places, and 16 had injuries caused by compressing or crushing. Eight patients had unilateral pubic bone fracture or pubic symphysis separation that involved posterior pelvic fracture or sacroiliac joint separation, and two had fractures that affected the anterior ring or acetabulum. Moreover, 26 patients had hemorrhagic shock, 18 had traumatic brain injury, 14 had fractures at other sites, 8 had pelvic large vessel injuries, 8 had ipsilateral femoral and proximal femoral fractures, 8 had retroperitoneal hematoma, 8 had urinary system injury, 6 had perineal laceration and vaginal trauma, 6 had spinal cord injury, 4 had intestinal injuries, 4 had soft tissue contusions, and 4 had sacral nerve injury. During the follow-up (average: 48 months), six children died. The evaluation results of the curative effect were excellent in 32 children, good in 18, and poor in 4; the 'excellent' and 'good' rate was 92.5% (50/54). CONCLUSION: Early diagnosis, reduction, and fixation and timely treatment of associated injuries might achieve better clinical efficacy and are worthy of clinical promotion. KEY WORDS: Associated Injuries, Childhood, Diagnosis, Fracture, Pelvic, Treatment.

[Impacts of arbuscular mycorrhizal fungi (AMF)on growth, N bio-fixation, and phosphorus uptake of legume crop.] / ä¸›æžèŒæ ¹çœŸèŒå¯¹è±†ç§‘ä½œç‰©ç”Ÿé•¿å’Œç”Ÿç‰©å›ºæ°®åŠç£·ç´ å¸æ”¶çš„å½±å“.

To explore the effects of arbuscular mycorrhizal fungi (AMF) on the growth of legume crop, pot and field experiments with soybean were conducted. Treatments of inoculation (+AMF) and non-inoculation with AMF (-AMF) were set up for the pot experiment, and AMF mycelium non-limited and limited for the field experiment. Results of the pot experiment showed that inoculation with AMF significantly increased soybean aboveground biomass (16.5%) and root nodules number (131.4%), above-ground plant phosphorus and nitrogen concentrations and uptakes. In the field trial, the above-ground and root biomasses and root nodules number under AMF mycelium non-limited were significantly increased by 123.6%, 61.5%, and 212.5% compared with those under the limited condition, respectively. Plant phosphorus uptake, nitrogen concentration and uptake, and soil available nitrogen and phosphorus concentrations were significantly higher under AMF mycelium non-limited than the limited both in both shoot and root. Our findings provide theoretical reference for further understanding the relationship between legume crop and AMF, as well as the efficient utilization of phosphorus fertilizer.

Fully Automatic Scar Segmentation for Late Gadolinium Enhancement MRI Images in Left Ventricle with Myocardial Infarction.

Numerous methods have been published to segment the infarct tissue in the left ventricle, most of them either need manual work, post-processing, or suffer from poor reproducibility. We proposed an automatic segmentation method for segmenting the infarct tissue in left ventricle with myocardial infarction. Cardiac images of a total of 60 diseased hearts (55 human hearts and 5 porcine hearts) were used in this study. The epicardial and endocardial boundaries of the ventricles in every 2D slice of the cardiac magnetic resonance with late gadolinium enhancement images were manually segmented. The subsequent pipeline of infarct tissue segmentation is fully automatic. The segmentation results with the automatic algorithm proposed in this paper were compared to the consensus ground truth. The median of Dice overlap between our automatic method and the consensus ground truth is 0.79. We also compared the automatic method with the consensus ground truth using different image sources from different centers with different scan parameters and different scan machines. The results showed that the Dice overlap with the public dataset was 0.83, and the overall Dice overlap was 0.79. The results show that our method is robust with respect to different MRI image sources, which were scanned by different centers with different image collection parameters. The segmentation accuracy we obtained is comparable to or better than that of the conventional semi-automatic methods. Our segmentation method may be useful for processing large amount of dataset in clinic.

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline.

Sepsis is a dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single-cell RNA-sequencing in a murine endotoxemia model revealed the involvement of various cell populations to be temporally organized and highly orchestrated. Endothelial and stromal cells were the first responders. At later time points, epithelial cells upregulated immune-related pathways while concomitantly downregulating physiological functions such as solute homeostasis. Sixteen hours after endotoxin, there was global cell-cell communication failure and organ shutdown. Despite this apparent organ paralysis, upstream regulatory analysis showed significant activity in pathways involved in healing and recovery. This rigorous spatial and temporal definition of murine endotoxemia will uncover precise biomarkers and targets that can help stage and treat human sepsis.

Ultrasound features predicting the 3-week outcome of Pavlik harness treatment for developmental hip dysplasia.

BACKGROUND: The treatment protocol for children with developmental dysplasia of the hip (DDH) is routinely adjusted by assessing the hip reduction after 3 weeks of Pavlik harness treatment. However, there is a high risk of failure and complications in the treatment adjustment. The aim of this study was to explore the value of ultrasound features in predicting the treatment outcome of Pavlik harness after 3 weeks in DDH children. METHODS: A total of 215 DDH children were recruited and the demographics and the changes of ultrasound features [α and ß angle and femoral head coverage (FHC)] during the Pavlik harness treatment were recorded. The children were divided into the success group and the failure group according to the reduction outcome after 3 weeks. Univariate and multivariate analyses were performed to analyze the independent predictors for the treatment outcome. Repeated-measures analysis of variance was used to compare the changes of ultrasound features between the two groups during the treatment. Receiver operating characteristic (ROC) curves were plotted to analyze the predictive accuracy of the ultrasound features. RESULTS: Graf type III (P=0.036), bilateral dislocation (P=0.031), and age at diagnosis (P=0.021) were associated with an increased risk of Pavlik harness failure in the multivariate analysis. The changes in α and ß angle and FHC were generally greater in the success group than in the failure group. The α angle and FHC were larger in the success group, while the ß angle was larger in the failure group (P<0.05). Each ultrasound parameter (α and ß angle and FHC) alone could not accurately predict the treatment outcome within 3 weeks. However, the combined ultrasonic features at the second week could accurately predict the outcome of Pavlik harness treatment after the third week. The combination of the ultrasound features at the first week and the influencing factors (Graf classification, age at diagnosis, and side of pathology) could accurately predict the outcome at the first week [area under curve (AUC) =0.931, sensitivity =82.14%, specificity =97.86%]. CONCLUSIONS: The combined model of ultrasonic features at the second week could accurately predict the reduction outcome of Pavlik harness after the third week. The combined model including independent predictors and ultrasonic features could accurately predict the reduction outcome at the first week.

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.

Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

The draft genome sequence of an upland wild rice species, Oryza granulata.

Exploiting novel gene sources from wild relatives has proven to be an efficient approach to advance crop genetic breeding efforts. Oryza granulata, with the GG genome type, occupies the basal position of the Oryza phylogeny and has the second largest genome (~882 Mb). As an upland wild rice species, it possesses renowned traits that distinguish it from other Oryza species, such as tolerance to shade and drought, immunity to bacterial blight and resistance to the brown planthopper. Here, we generated a 736.66-Mb genome assembly of O. granulata with 40,131 predicted protein-coding genes. With Hi-C data, for the first time, we anchored ~98.2% of the genome assembly to the twelve pseudo-chromosomes. This chromosome-length genome assembly of O. granulata will provide novel insights into rice genome evolution, enhance our efforts to search for new genes for future rice breeding programmes and facilitate the conservation of germplasm of this endangered wild rice species.