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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.
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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.
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Poaceae , Tetraploidia , Poaceae/genética , Poliploidia , Genômica , Transcriptoma/genética , Genoma de Planta/genética , Evolução MolecularRESUMO
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.
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Brassicaceae , Genoma de Planta , Cariótipo , Filogenia , Brassicaceae/genética , Evolução Molecular , Cromossomos de Plantas/genéticaRESUMO
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.
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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.
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Terapia por Acupuntura , Eletroacupuntura , Gastroenteropatias , Ratos , Animais , Humanos , Eletroacupuntura/métodos , Ratos Sprague-Dawley , Pontos de Acupuntura , Gastroenteropatias/genética , Gastroenteropatias/terapiaRESUMO
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.
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Fraturas Ósseas , Ossos Pélvicos , Fraturas da Coluna Vertebral , Acidentes de Trânsito , Adolescente , Criança , Pré-Escolar , Feminino , Fraturas Ósseas/diagnóstico , Fraturas Ósseas/etiologia , Fraturas Ósseas/terapia , Humanos , Masculino , Ossos Pélvicos/lesões , Ossos Pélvicos/cirurgia , Estudos RetrospectivosRESUMO
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.
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Fabaceae , Micorrizas , Nitrogênio , Fósforo , Raízes de PlantasRESUMO
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.
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Cicatriz/diagnóstico por imagem , Gadolínio/química , Ventrículos do Coração/diagnóstico por imagem , Ventrículos do Coração/patologia , Interpretação de Imagem Assistida por Computador , Imageamento por Ressonância Magnética , Infarto do Miocárdio/diagnóstico por imagem , Animais , Automação , Humanos , SuínosRESUMO
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.
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Evolução Biológica , Genoma de Planta , Poaceae/genética , Composição de Bases , Cromossomos de Plantas , Flores/genética , Flores/crescimento & desenvolvimento , Duplicação Gênica , Família Multigênica , Filogenia , Proteínas de Plantas/genéticaRESUMO
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.
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Endotoxemia/etiologia , Endotoxinas/metabolismo , Rim/metabolismo , Sepse/etiologia , Adulto , Idoso , Animais , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Pessoa de Meia-Idade , Adulto JovemRESUMO
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.].
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Genoma de Cloroplastos , Ásia Oriental , Marcadores Genéticos , Filogenia , Poaceae/genéticaRESUMO
African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately â¼363.5 Mb, representing â¼92.7% of the estimated African wild rice genome (â¼392 Mb). The N50 lengths of the assembled contigs and scaffolds were â¼46.49 Kb and â¼6.83 Mb, indicating â¼3.72-fold and â¼18.8-fold improvement in length compared to the earlier released assembly (â¼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.
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Oryza , Genoma , Genômica , Oryza/genética , Análise de Sequência de DNARESUMO
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.
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Ginsenosídeos/biossíntese , Ginsenosídeos/genética , Panax notoginseng/genética , Transcriptoma/genética , Processamento Alternativo/genética , Flores/genética , Flores/metabolismo , Flores/fisiologia , Perfilação da Expressão Gênica/métodos , Genes de Plantas/genética , Ginsenosídeos/metabolismo , Anotação de Sequência Molecular/métodos , Panax/genética , Panax/metabolismo , Panax notoginseng/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/fisiologia , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Raízes de Plantas/fisiologia , RNA-Seq/métodos , Rizoma/genética , Rizoma/metabolismo , Rizoma/fisiologia , Sapogeninas/metabolismo , Saponinas/genética , Saponinas/metabolismo , Sequenciamento do Exoma/métodosRESUMO
Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.
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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.
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Displasia do Desenvolvimento do Quadril , Luxação Congênita de Quadril , Criança , Luxação Congênita de Quadril/diagnóstico por imagem , Luxação Congênita de Quadril/terapia , Humanos , Lactente , Aparelhos Ortopédicos , Estudos Retrospectivos , Resultado do Tratamento , UltrassonografiaRESUMO
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.
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Genoma de Planta , Oryza/genética , Fenótipo , Filogenia , Melhoramento VegetalRESUMO
Asian cultivated rice is believed to have been domesticated from a wild progenitor, Oryza rufipogon, offering promising sources of alleles for world rice improvement. Here we first present a high-quality chromosome-scale genome of the typical O. rufipogon. Comparative genomic analyses of O. sativa and its two wild progenitors, O. nivara and O. rufipogon, identified many dispensable genes functionally enriched in the reproductive process. We detected millions of genomic variants, of which large-effect mutations could affect agronomically relevant traits. We demonstrate how lineage-specific expansion of gene families may have contributed to the formation of reproduction isolation. We document thousands of genes with signatures of positive selection that are mainly involved in the reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as forces to govern substantial genomic alterations that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats.
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Evolução Molecular , Perfilação da Expressão Gênica , Genes de Plantas , Genoma de Planta , Oryza/genética , Imagem Individual de Molécula , Ecossistema , Regulação da Expressão Gênica de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Oryza/crescimento & desenvolvimento , Filogenia , Seleção Genética , Especificidade da Espécie , TranscriptomaRESUMO
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.
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Enzimas Imobilizadas , Nanopartículas de Magnetita/química , Polietilenoglicóis/química , Animais , Estabilidade Enzimática , Enzimas Imobilizadas/química , Enzimas Imobilizadas/metabolismo , Enzimas Imobilizadas/farmacocinética , Tamanho da Partícula , Ratos , Ratos Sprague-Dawley , beta-Glucosidase/química , beta-Glucosidase/metabolismo , beta-Glucosidase/farmacocinéticaRESUMO
The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the â¼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by â¼65.88% (â¼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains â¼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.