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BACKGROUND: Previous research has demonstrated that neuroinflammation is a key element in the progress of epilepsy. Nevertheless, it is currently unidentified which inflammatory factors and proteins increase or decrease the risk of epilepsy. METHODS: We adopted Mendelian randomization techniques to explore the causal relationship between circulating inflammatory factors and proteins and various epilepsy. Our principal approach was inverse variance weighting, supplemented by several sensitivity analyses to guarantee the robustness of our findings. RESULTS: Studies have identified associations between epilepsy and specific inflammatory factors and proteins: three inflammatory factors and six proteins are linked to epilepsy in general; one inflammatory factor and four proteins are associated with focal epilepsy with no documented lesions; two inflammatory factors and three proteins are related to focal epilepsy, excluding cases with hippocampal sclerosis; two inflammatory factors and two proteins are connected to juvenile myoclonic epilepsy; two inflammatory factors and five proteins are linked to juvenile absence epilepsy; four inflammatory proteins are associated with childhood absence epilepsy; two inflammatory factors are related to focal epilepsy overall; two inflammatory factors and two proteins are connected to generalized epilepsy; and two inflammatory proteins are linked to generalized epilepsy with tonic-clonic seizures. Additionally, six inflammatory factors may play a downstream role in focal epilepsy. CONCLUSION: Our study uncovers various inflammatory factors and proteins that influence the risk of epilepsy, offering instructive insights to the diagnosis and therapy of the condition.
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Citocinas , Epilepsia , Análisis de la Aleatorización Mendeliana , Humanos , Epilepsia/sangre , Epilepsia/genética , Citocinas/sangre , Inflamación/sangreRESUMEN
Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.
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Cycadopsida , Magnoliopsida , Hibridación Fluorescente in Situ , Cycadopsida/genética , Telómero/genética , Centrómero/genética , Magnoliopsida/genéticaRESUMEN
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Variación Genética , Polimorfismo Genético , Animales , ADN Ribosómico/genética , Mutación , Hongos/genética , Evolución Molecular , FilogeniaRESUMEN
Organosulfates (OSs) could be potentially important compounds in marine organic aerosols, while their formation in marine atmospheres is far from clear due to a lack of cruise observations. In this work, shipboard atmospheric observations were conducted over the Yellow Sea and Bohai Sea to investigate the abundance and formation of biogenic isoprene/monoterpene-OSs in marine aerosols. The quantified OSs and NOSs accounted for 0.04-6.9% of marine organic aerosols and were 0.07-2.2% of the non-sea-salt (nss) sulfate in terms of sulfur content. Isoprene-related (nitrooxy-)OSs occupied 27-87% of the total quantified OSs, following the abundance order of summer > autumn > spring or winter. This order was driven by the marine phytoplankton biomass and sea surface temperature (SST), which controlled the seawater and atmospheric isoprene concentration levels. Under the severe impacts of anthropogenic pollutants from the East Asia continent in winter, monoterpene nitrooxy-OSs, generated with NOx involved in, increased to 34.4 ± 35.5 ng/m3 and contributed 68% of the quantified (nitrooxy-)OSs. Our results highlight the notable roles of biogenic OSs in marine organic aerosols over regions with high biological activity and high SST. The formation of biogenic OSs and their roles in altering marine aerosol properties calls for elaboration through cruise observations in different marine environments.
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Contaminantes Atmosféricos , Contaminantes Ambientales , Fitoplancton , Contaminantes Atmosféricos/análisis , Monoterpenos , Aerosoles/análisisRESUMEN
Plant-derived exosome-like nanoparticles(PELNs) are a class of membranous vesicles with diameters approximately ranging from 30 to 300 nm, isolated from plant tissues. They contain components such as proteins, lipids, and nucleic acids. PELNs play an important role in the metabolism of plant substances and immune defense, and can also cross-regulate the physiological activities of fungi and animal cells, showing significant potential applications. In recent years, research on PELNs has significantly increased, highlighting three main issues:(1) the mixed sources of plant materials for PELNs;(2) the lack of a unified system for isolating and characterizing PELNs;(3) the urgent need to elucidate the molecular mechanisms underlying the cross-regulation of biological functions by PELNs. This article focused on these concerns. It began by summarizing the biological origin and composition of PELNs, discussing the techniques for isolating and characterizing PELNs, and analyzing their biomedical applications and potential future research directions., aiming to promote the establishment of standardized research protocols for PELNs and provide theoretical references for in-depth exploration of the mechanisms underlying PELNs' cross-regulatory effects.
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Exosomas , Nanopartículas , Ácidos Nucleicos , Animales , Exosomas/metabolismo , Proteínas/metabolismo , Plantas/metabolismoRESUMEN
As a new energy source for atrial fibrillation ablation, electric pulse ablation has higher tissue selectivity and biosafety, so it has a great application prospect. At present, there is very limited research on multi-electrode simulated ablation of histological electrical pulse. In this study, a circular multi-electrode ablation model of pulmonary vein will be built on COMSOL5.5 platform for simulation research. The results show that when the voltage amplitude reaches about 900 V, it can make some positions achieve transmural ablation, and the depth of continuous ablation area formed can reach 3 mm when the voltage amplitude reaches 1 200 V. When the distance between catheter electrode and myocardial tissue is increased to 2 mm, a voltage of at least 2 000 V is required to make the depth of continuous ablation area reach 3 mm. Through the simulation of electric pulse ablation with ring electrode, the research results of this project can provide reference for the voltage selection in the clinical application of electric pulse ablation.
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Fibrilación Atrial , Ablación por Catéter , Humanos , Frecuencia Cardíaca , Fibrilación Atrial/cirugía , Electrodos , ElectricidadRESUMEN
Polysiloxanes have attracted considerable attention in biomedical engineering, owing to their inherent properties, including good flexibility and biocompatibility. However, their low mechanical strength limits their application scope. In this study, we synthesized a polysiloxane-based polyurethane by chemical copolymerization. A series of thermoplastic polysiloxane-polyurethanes (Si-TPUs) was synthesized using hydroxyl-terminated polydimethylsiloxane containing two carbamate groups at the tail of the polymer chains 4,4'-dicyclohexylmethane diisocyanate (HMDI) and 1,4-butanediol as raw materials. The effects of the hard-segment content and soft-segment number average molecular weight on the properties of the resulting TPUs were investigated. The prepared HMDI-based Si-TPUs exhibited good microphase separation, excellent mechanical properties, and acceptable repeatable processability. The tensile strength of SiTPU-2K-39 reached 21.5 MPa, which is significantly higher than that of other flexible polysiloxane materials. Moreover, the tensile strength and breaking elongation of SiTPU-2K-39 were maintained at 80.9% and 94.6%, respectively, after three cycles of regeneration. The Si-TPUs prepared in this work may potentially be used in gas separation, medical materials, antifouling coatings, and other applications.
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Poliuretanos , Siloxanos , Poliuretanos/química , Siloxanos/química , Materiales Biocompatibles/química , Resistencia a la Tracción , Polímeros/química , DimetilpolisiloxanosRESUMEN
BACKGROUND: A significant challenge in cancer therapy is to maximize the therapeutic efficacy and minimize the side effects. In the past decade, a lot of nanoparticles have been used as the carriers for efficient drug delivery. METHODS AND RESULTS: This study was to prepare R9 modified with 125I-labeled cRGD and ce6 which self-assembled with miR-139-5p to form nanoparticles (Ce6-R9-125I-RGD-MNPs), and to further take advantage of the enhanced permeability and retention (EPR) effect of radiolabeled nanoparticles to realize the integration of tumor diagnosis and treatment. We successfully synthesized and represented it, saline and serum stability experiments demonstrating good stability. Moreover, Ce6-R9-125I-RGD-MNPs showed superior tumor targeting and the effect of combined photodynamic therapy (PDT) and radiotherapy treatment in vivo and vitro. CONCLUSION: The pathological results further confirmed that the therapeutic doses of Ce6-R9-125I-RGD-MNPs cause pathological changes of tumor tissues while showing minimal toxicity to normal tissues.
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Antineoplásicos/farmacología , Sistemas de Liberación de Medicamentos , MicroARNs/química , Neoplasias/terapia , Péptidos/farmacología , Fotoquimioterapia , Fármacos Fotosensibilizantes/farmacología , Antineoplásicos/síntesis química , Antineoplásicos/química , Relación Dosis-Respuesta a Droga , Humanos , Radioisótopos de Yodo , Estructura Molecular , Nanopartículas/química , Péptidos/síntesis química , Péptidos/química , Procesos Fotoquímicos , Fármacos Fotosensibilizantes/síntesis química , Fármacos Fotosensibilizantes/química , Relación Estructura-ActividadRESUMEN
INTRODUCTION: Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. METHODS: We applied high-throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic homogeneity. In addition, fluorescent in situ hybridization and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of rDNA. KEY RESULTS: The 5S and 35S rRNA genes were separate (S-type) in Gnetum montanum, Gnetum gnemon and Welwitschia mirabilis and linked (L-type) in Ephedra altissima. There was considerable variability in 5S rDNA abundance, ranging from as few as ~4000 (W. mirabilis) to >100 000 (G. montanum) copies. A similar large variation was also observed in 5S rDNA locus numbers (two to 16 sites per diploid cell). 5S rRNA pseudogenes were interspersed between functional genes forming a single unit in E. altissima and G. montanum. Their copy number was comparable or even higher than that of functional 5S rRNA genes. In E. altissima internal transcribed spacers of 35S rDNA were long and intrinsically repetitive while in G. montanum and W. mirabilis they were short without the subrepeats. CONCLUSIONS: Gnetophytes are distinct from other gymnosperms and angiosperms as they display surprisingly large variability in rDNA organization and rDNA copy and locus numbers between genera, with no relationship between copy numbers and genome sizes apparent. Concerted evolution of 5S rDNA units seems to have led to the amplification of 5S pseudogenes in both G. montanum and E. altissima. Evolutionary patterns of rDNA show both gymnosperm and angiosperm features underlining the diversity of the group.
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Cycadopsida , Variaciones en el Número de Copia de ADN , ADN Ribosómico , Evolución Molecular , Hibridación Fluorescente in Situ , FilogeniaRESUMEN
It is very important to understand the molecular mechanism of the fracture behavior of chemically cross-linked polymer nanocomposites (PNCs). Thus, in this work, by employing a coarse-grained molecular dynamics simulation we investigated the effect of the cross-link density and the cross-link distribution on it by calculating the void formation and the chemical bond scission. Considering the fracture energy, the optimal fracture properties of PNCs are realized at the moderate cross-link density which results from the competition between the chain slippage induced voids and the bond scission induced voids. Meanwhile, more bond scission occurs on the chain backbone while a high broken percentage of the cross-link bonds appears between chains because of the higher average stress borne by one cross-linked bead than by one other bead. In addition, the number of voids is quantified which first increases and then decreases with the strain at low cross-link density. However, the number of newly formed voids increases again at high cross-link density. Finally, it decreases because of the low rate of bond scission. Furthermore, the chemical bonds are broken at a similar strain for the uniform cross-link distribution while they are broken at any strain for the nonuniform cross-link distribution. The low number of broken bonds induces the disappearance of the second peak of the number of voids with the strain for the nonuniform cross-link distribution. In summary, this work could provide a clear understanding of the fracture mechanism of the chemically cross-linked PNCs on the molecular level.
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By employing coarse-grained molecular dynamics simulations, we investigated the fracture behavior of polymer nanocomposites (PNCs) filled with polymer-grafted nanoparticles (NPs) in detail by particularly regulating the grafting density and the length of the grafted chain. By calculating their fracture energy, we observed that their rupture properties first increase and then decrease with the increase of the grafting density or the length of the grafted chains. Their bond orientation degree and their van der Waals energy change are characterized to understand their fracture behavior. To further explain it, we analyzed the contributions of the matrix chains, grafted chains, and NPs to the total stress. It is interesting to find that the stress borne by one bead of matrix chains or NPs gradually increases with the grafting density, while the stress borne by the grafted chains first increases and then decreases. In addition, the stress borne by one bead of matrix chains or grafted chains gradually increases with the length of the grafted chains, while the stress borne by NPs remains nearly unchanged. As a result of these contributions, the optimal fracture properties appear at the moderate grafting density or length of the grafted chain. Then, the number of voids is quantified, which first increases and then decreases with strain because of the coalescence of small voids into large ones. Accompanying this, the maximum void size increases significantly. Furthermore, the maximum number of voids increases with the grafting density, while it is nearly independent of the length of the grafted chain. In particular, the voids are preferably generated at the end beads of the chains or at the surfaces of the NPs. In summary, this work could provide some further understanding of how the grafted chains affect the fracture properties of the PNCs.
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Lysine methylation of chromosomal and nuclear proteins is a well-known mechanism of epigenetic regulation, but relatively little is known about the role of this protein modification in signal transduction. Using an RNAi-based functional screening of the SMYD family of lysine methyltransferases (KMTs), we identified SMYD2 as a KMT essential for robust bone morphogenic protein (BMP)- but not TGFß-induced target gene expression in HaCaT keratinocyte cells. A role for SMYD2 in BMP-induced gene expression was confirmed by shRNA knockdown and CRISPR/Cas9-mediated knock-out of SMYD2 We further demonstrate that SMYD2 knockdown or knock-out impairs BMP-induced phosphorylation of the signal-transducing protein SMAD1/5 and SMAD1/5 nuclear localization and interaction with SMAD4. The SMYD2 KMT activity was required to facilitate BMP-mediated signal transduction, as treatment with the SMYD2 inhibitor AZ505 suppressed BMP2-induced SMAD1/5 phosphorylation. Furthermore, we present evidence that SMYD2 likely modulates the BMP response through its function in the cytosol. We show that, although SMYD2 interacted with multiple components in the BMP pathway, it specifically methylated the kinase domain of BMP type II receptor BMPR2. Taken together, our findings suggest that SMYD2 may promote BMP signaling by directly methylating BMPR2, which, in turn, stimulates BMPR2 kinase activity and activation of the BMP pathway.
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Receptores de Proteínas Morfogenéticas Óseas de Tipo II/química , Receptores de Proteínas Morfogenéticas Óseas de Tipo II/metabolismo , Proteínas Morfogenéticas Óseas/metabolismo , N-Metiltransferasa de Histona-Lisina/metabolismo , Transducción de Señal , Línea Celular , Células HEK293 , Humanos , Metilación , Dominios ProteicosRESUMEN
Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.
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Eucommiaceae/genética , Genoma del Cloroplasto/genética , ADN de Cloroplastos/genética , Evolución Molecular , Genética de Población , Mutación/genética , FilogeniaRESUMEN
Herbaceous bamboos (Olyreae) are a separate lineage with idiosyncratic traits, e.g., unisexual flowers and annual or seasonal flowering lifestyle, in the grass family. To elucidate the evolution of herbaceous bamboos we produced two complete chloroplast (cp) genomes from two monotypic genera i.e., Froesiochloa and Rehia via the genome-skimming approach. The assembled F. boutelouoides and R. nervata cp genomes were 135,905 and 136,700 base-pair (bp), respectively. Further whole-genome comparative analyses revealed that the cp genes order was perfectly collinear, but the inverted repeats (IRs) borders, i.e., the junctions between IRs and single copy regions, were highly divergent in Olyreae. The IRs expansions/contractions occurred frequently in Olyreae, which have caused gene content and genome size variations, e.g., the copy number reduction of rps19 and trnH(GUG) genes in Froesiochloa. Subsequent nucleotide mutation analyses uncovered a greatly heterogeneous divergence pattern among different cpDNA regions in Olyreae cp genomes. On average, non-coding loci evolved at a rate of circa 1.9 times faster than coding loci, from which 20 rapidly evolving loci were determined as potential genetic markers for further studies on Olyreae. In addition, the phylogenomic analyses from 67 grass plastomes strongly supported the phylogenetic positions of Froesiochloa and Rehia in the Olyreae.
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Genoma del Cloroplasto , Genoma de Planta , Secuencias Invertidas Repetidas/genética , Mutación/genética , Poaceae/genética , Teorema de Bayes , Mapeo Cromosómico , Sitios Genéticos , Marcadores Genéticos , Funciones de Verosimilitud , Anotación de Secuencia Molecular , Filogenia , Polimorfismo de Nucleótido Simple/genéticaRESUMEN
As one of the major active ingredients in Radix Scutellariae, wogonin has been shown to be associated with various pharmacological activities on cancer cell growth, apoptosis, and cell invasion and migration. Here, we demonstrated that wogonin may harbor potential anti-metastatic activities in hepatocarcinoma (HCC). The anti-metastasis potential of wogonin and its underlying mechanisms were evaluated by ligand-protein docking approach, surface plasmon resonance assay, and in vitro gelatin zymography studies. Our results showed that wogonin (100 µM, 50 µM) suppressed MHCC97L and PLC/PRF/5 cells migration and invasion in vitro. The docking approach and surface plasmon resonance assay indicated that the potential binding affinity between wogonin and matrix metalloproteinase-9 (MMP-9) may lead to inhibition of MMP-9 activity and further leads to suppression of tumor metastasis. This conclusion was further verified by Western blot results and gelatin zymography analysis. Wogonin might be a potent treatment option for disrupting the tumor metastasis that favors HCC development. The potential active targets from computational screening integrated with biomedical study may help us to explore the molecular mechanism of herbal medicines.
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Antineoplásicos Fitogénicos/farmacología , Flavanonas/farmacología , Regulación Neoplásica de la Expresión Génica , Hepatocitos/efectos de los fármacos , Metaloproteinasa 9 de la Matriz/genética , Scutellaria baicalensis/química , Antineoplásicos Fitogénicos/química , Sitios de Unión , Línea Celular Tumoral , Ensayos de Migración Celular , Movimiento Celular/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Flavanonas/química , Hepatocitos/enzimología , Hepatocitos/patología , Humanos , Molécula 1 de Adhesión Intercelular/genética , Molécula 1 de Adhesión Intercelular/metabolismo , Metaloproteinasa 9 de la Matriz/química , Metaloproteinasa 9 de la Matriz/metabolismo , Simulación del Acoplamiento Molecular , Proteínas de Neoplasias/antagonistas & inhibidores , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Transducción de Señal , Molécula de Interacción Estromal 1/antagonistas & inhibidores , Molécula de Interacción Estromal 1/genética , Molécula de Interacción Estromal 1/metabolismoRESUMEN
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Cycas/genética , ADN de Plantas/genética , ADN Ribosómico/genética , ARN Ribosómico 18S/genética , ARN Ribosómico 5.8S/genética , ARN Ribosómico/genética , Secuencia de Bases , ADN Espaciador Ribosómico/genética , Hibridación Fluorescente in Situ , Polimorfismo de Nucleótido Simple/genética , Análisis de Secuencia de ADN , Transcripción Genética/genéticaRESUMEN
Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.
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Eucommiaceae/genética , Perfilación de la Expresión Génica/métodos , Óvulo Vegetal/genética , Proteínas de Plantas/genética , Polen/genética , Eucommiaceae/crecimiento & desarrollo , Flores/genética , Flores/crecimiento & desarrollo , Regulación de la Expresión Génica de las Plantas , Secuenciación de Nucleótidos de Alto Rendimiento , Especificidad de Órganos , Hojas de la Planta/genética , Hojas de la Planta/crecimiento & desarrollo , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ARNRESUMEN
Isocitrate dehydrogenase (IDH) is a key enzyme in the tricarboxylate (TCA) cycle, which may play an important role in the virulence of pathogenic bacteria. Here, two structurally different IDHs from a plant pathogen Xanthomonas campestris pv. campestris 8004 (XccIDH1 and XccIDH2) were characterized in detail. The recombinant XccIDH1 forms homodimer in solution, while the recombinant XccIDH2 is a typical monomer. Phylogenetic analysis showed that XccIDH1 belongs to the type I IDH subfamily and XccIDH2 groups into the monomeric IDH clade. Kinetic characterization demonstrated that XccIDH1's specificity towards NAD(+) was 110-fold greater than NADP(+) , while XccIDH2's specificity towards NADP(+) was 353-fold greater than NAD(+) . The putative coenzyme discriminating amino acids (Asp268, Ile269 and Ala275 for XccIDH1, and Lys589, His590 and Arg601 for XccIDH2) were studied by site-directed mutagenesis. The coenzyme specificities of the two mutants, mXccIDH1 and mXccIDH2, were completely reversed from NAD(+) to NADP(+) , and NADP(+) to NAD(+) , respectively. Furthermore, Ser80 of XccIDH1, and Lys256 and Tyr421 of XccIDH2, were the determinants for the substrate binding. The detailed biochemical properties, such as optimal pH and temperature, thermostability, and metal ion effects, of XccIDH1 and XccIDH2 were further investigated. The possibility of taking the two IDHs into consideration as the targets for drug development to control the plant diseases caused by Xcc 8004 were described and discussed thoroughly.
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Isocitrato Deshidrogenasa/metabolismo , Enfermedades de las Plantas/microbiología , Proteínas Recombinantes/metabolismo , Xanthomonas campestris/enzimología , Xanthomonas campestris/patogenicidad , Secuencia de Aminoácidos , Sitios de Unión , Biología Computacional , Isocitrato Deshidrogenasa/genética , Cinética , NAD/metabolismo , NADP/metabolismo , Filogenia , Proteínas Recombinantes/genética , Alineación de Secuencia , Especificidad por SustratoRESUMEN
The development of efficient, rapid, portable, and accurate analysis of veterinary drug residues in food matrices is in great demand for food safety assessment. Here, we have developed a smartphone-integrated platform for fluorometric quantification of metronidazole (MNZ) residues and constructed a sensor array for discrimination of different nitroimidazole antibiotics (NIIMs). Multicolor CDs (B-CDs, C-CDs, Y-CDs, and R-CD) were prepared and showed different fluorescence response to MNZ. The fluorescence of C-CDs was quenched Because of the inner filter eï¬ect (IFE) between the C-CDs and MNZ, while that of R-CDs was enhanced due to the passivation of surface defects by MNZ. Based on the response pattern, the fluorometric quantification of MNZ based on the fluorescence images of C-CD + R-CD system (R/G values) was achieved with a low detection limit of 0.45 µM. By designing a smartphone-integrated platform, the analysis can be completed within 20 min. In addition, a ï¬uorescence sensor array based C-CDs and R-CDs was also developed. The unique fingerprint of each NIIMs was obtained by linear discriminant analysis (LDA) of the response patterns, indicating an effective discrimination of five NIIMs. Moreover, the platform was used for quantification of MNZ in food samples and the recoveries were within 84.0-106.3 % with relative standard deviations 1.2-10.2 %. Therefore, the proposed method shows great potential as a universal platform for rapid detection of veterinary drug residues.