Chromosome doubling increases PECTIN METHYLESTERASE 2 expression, biomass, and osmotic stress tolerance in kiwifruit.

Chromosome doubling-induced polyploidization is a popular tool for crop breeding. Polyploidy crops commonly have multiple advantages, including increased biomass and stress tolerance. However, little is known about the genes responsible for these advantages. We found kiwifruit (Actinidia chinensis cv. Hongyang) PECTIN METHYLESTERASE 2 (AcPME2)is substantially upregulated in artificially created tetraploid plants that show increased biomass and enhanced tolerance to osmotic stress. Overexpression (OE) of AcPME2 led to increased biomass and enhanced stress tolerance in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), and kiwifruit. Upon short-term osmotic stress treatment, AcPME2-OE plants showed higher levels of demethylesterified pectins and more Ca2+ accumulation in the cell wall than Col-0 plants, which led to increased cell wall stiffness. The stress-induced plasmolysis assays indicated that AcPME2 dynamically mediated the cell wall stiffness in response to osmotic stress, which is dependent on Ca2+ accumulation. Transcriptomic analysis discovered that dozens of stress-responsive genes were significantly upregulated in the AcPME2-OE plants under osmotic stress. Besides, AcPME2-mediated cell wall reinforcement prevented cell wall collapse and deformation under osmotic stress. Our results revealed a single gene contributes to two advantages of polyploidization (increased biomass and osmotic stress tolerance) and that AcPME2 dynamically regulates cell wall stiffness in response to osmotic stress.

Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear.

Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height.

NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m5C methylation.

BACKGROUND: Diabetic retinopathy (DR) is the leading cause of blinding eye disease among working adults and is primarily attributed to the excessive proliferation of microvessels, which leads to vitreous hemorrhage and retinal traction, thereby significantly impairing patient vision. NSUN2-mediated RNA m5C methylation is implicated in various diseases, and in this investigation, we focused on elucidating the impact of NSUN2 on the regulation of the expression of the downstream gene MUC1, specifically through RNA m5C methylation, on the progression of DR. METHOD: Utilizing Microarray analysis, we examined patient vitreous fluid to pinpoint potential therapeutic targets for DR. Differential expression of NSUN2 was validated through qRT-PCR, Western blot, and immunofluorescence in human tissue, animal tissue, and cell model of DR. The relationship between NSUN2 and DR was explored in vitro and in vivo through gene knockdown and overexpression. Various techniques, such as MeRIP-qPCR and dot blot, were applied to reveal the downstream targets and mechanism of action of NSUN2. RESULTS: The levels of both NSUN2 and RNA m5C methylation were significantly elevated in the DR model. Knockdown of NSUN2 mitigated DR lesion formation both in vitro and in vivo. Mechanistically, NSUN2 promoted MUC1 expression by binding to the RNA m5C reader ALYREF. Knockdown of ALYREF resulted in DR lesion alterations similar to those observed with NSUN2 knockdown. Moreover, MUC1 overexpression successfully reversed a series of DR alterations induced by NSUN2 silencing. CONCLUSIONS: NSUN2 regulates the expression of MUC1 through ALYREF-mediated RNA m5C methylation, thereby regulating the progression of DR and providing a new option for the treatment of DR in the future.

Genomic insights into domestication and genetic improvement of fruit crops.

Fruit crops cultivated in almost all countries and regions around the world serve as important agricultural commodities of significant economic value because they contribute to overall food security by providing a diverse food and nutrient supply to sustain human life and human health. Recent advances in high-throughput sequencing technologies offer unprecedented opportunities for pursuing genomic and genetic studies of fruit crops. Here, we will review major advances in fruit crop genome sequencing efforts undertaken over the past 15 years that have contributed to significant accumulation of publicly available genomic resources. We will highlight the expanding pool of genomic data that offer unprecedented opportunities to better unravel the genetic origin and domestication of fruit trees, as well as in deciphering the genetics of important horticultural traits of these fruit trees. Furthermore, we will explore how utilization of these genetic features of fruit trees along with new genomic-assisted tools, including genomic selection and gene editing, are informing and guiding plant geneticists and breeders in moving forward in their fruit crop breeding efforts. Finally, we will outline future prospects and unresolved questions that remain in both genomic research and genetic improvement of fruit crops.

The transcription factor PbrMYB24 regulates lignin and cellulose biosynthesis in stone cells of pear fruits.

Lignified stone cell content is a key factor used to evaluate fruit quality, influencing the economic value of pear (Pyrus pyrifolia) fruits. However, our understanding of the regulatory networks of stone cell formation is limited due to the complex secondary metabolic pathway. In this study, we used a combination of co-expression network analysis, gene expression profiles, and transcriptome analysis in different pear cultivars with varied stone cell content to identify a hub MYB gene, PbrMYB24. The relative expression of PbrMYB24 in fruit flesh was significantly correlated with the contents of stone cells, lignin, and cellulose. We then verified the function of PbrMYB24 in regulating lignin and cellulose formation via genetic transformation in homologous and heterologous systems. We constructed a high-efficiency verification system for lignin and cellulose biosynthesis genes in pear callus. PbrMYB24 transcriptionally activated multiple target genes involved in stone cell formation. On the one hand, PbrMYB24 activated the transcription of lignin and cellulose biosynthesis genes by binding to different cis-elements [AC-I (ACCTACC) element, AC-II (ACCAACC) element and MYB-binding sites (MBS)]. On the other hand, PbrMYB24 bound directly to the promoters of PbrMYB169 and NAC STONE CELL PROMOTING FACTOR (PbrNSC), activating the gene expression. Moreover, both PbrMYB169 and PbrNSC activated the promoter of PbrMYB24, enhancing gene expression. This study improves our understanding of lignin and cellulose synthesis regulation in pear fruits through identifying a regulator and establishing a regulatory network. This knowledge will be useful for reducing the stone cell content in pears via molecular breeding.

Relationship between 24-h activity behavior and body fat percentage in preschool children: based on compositional data and isotemporal substitution analysis.

OBJECTIVE: This study aims to elucidate the dose‒response relationship between 24-h activity behaviors and body fat percentage (BFP) in Chinese preschool children using a compositional isotemporal substitution model (ISM). METHODS: In a cross-sectional design, 881 children aged 3-6 from urban and rural areas of Jiangxi Province were sampled. Activity behaviors, including sedentary behavior (SB), low-intensity physical activity (LPA), and moderate- to high-intensity physical activity (MVPA), were measured using accelerometers. Sleep patterns were assessed through questionnaires, and BFP was determined by bioelectrical impedance analysis (BIA). The study employed compositional data analysis (CoDA) and ISM to estimate the impact of reallocating durations of different activity behaviors on BFP. RESULTS: Higher BFP was found in urban vs. rural children, decreasing with age. Overweight and obesity rates were 10.6% and 7.6%, respectively, above national averages. MVPA and LPA were negatively correlated with BFP, while SB was positively correlated. A 30-min MVPA reduction significantly increased zBFR, particularly in overweight children. Gender-specific nuances revealed that boys' MVPA negatively influenced zBFP (ß = -0.155), P < 0.05), while girls' SB positively impacted zBFP (ß = 0.636, P < 0.01). Isotemporal simulations emphasized amplified effects in overweight children, with boys' zBFR rising rapidly when MVPA was substituted and girls displaying a notable substitution effect between SB and LPA. CONCLUSION: BFP is closely linked to 24-h activity behaviors, notably in overweight and obese preschoolers. ISM identified MVPA as a critical influencer, with a 30-min reduction substantially increasing BFP. Gender disparities were evident, implicating MVPA in boys and LPA and SB in girls.

Lead-212/Bismuth-212 In Vivo Generator Based on Ultrasmall Silver Telluride Nanoparticles.

Radionuclide therapy employing alpha emitters holds great potential for personalized cancer treatment. However, certain challenges remain when designing alpha radiopharmaceuticals, including the lack of stability of used radioconjugates due to nuclear decay events. In this work, ultrasmall silver telluride nanoparticles with a core diameter of 2.1 nm were prepared and radiolabeled with lead-212 using a chelator-free method with a radiolabeling efficiency of 75%. The results from the in vitro radiochemical stability assay indicated a very high retention of bismuth-212 despite the internal conversion effects originating from the decay of 212Pb. To further evaluate the potential of the nanoparticles, they were radiolabeled with indium-111, and their cell uptake and subcellular distribution were determined in 2D U87 cells, showing accumulation in the nucleus. Although not intentional, it was observed that the indium-111-radiolabeled nanoparticles induced efficient tumor cell killing, which was attributed to the Auger electrons emitted by indium-111. Combining the results obtained in this work with other favorable properties such as fast renal clearance and the possibility to attach targeting vectors on the surface of the nanoparticles, all well-known from the literature, these ultra-small silver telluride nanoparticles provide exciting opportunities for the design of theragnostic radiopharmaceuticals.

Molecular mechanisms of tumor resistance to radiotherapy.

BACKGROUND: Cancer is the most prevalent cause of death globally, and radiotherapy is considered the standard of care for most solid tumors, including lung, breast, esophageal, and colorectal cancers and glioblastoma. Resistance to radiation can lead to local treatment failure and even cancer recurrence. MAIN BODY: In this review, we have extensively discussed several crucial aspects that cause resistance of cancer to radiation therapy, including radiation-induced DNA damage repair, cell cycle arrest, apoptosis escape, abundance of cancer stem cells, modification of cancer cells and their microenvironment, presence of exosomal and non-coding RNA, metabolic reprogramming, and ferroptosis. We aim to focus on the molecular mechanisms of cancer radiotherapy resistance in relation to these aspects and to discuss possible targets to improve treatment outcomes. CONCLUSIONS: Studying the molecular mechanisms responsible for radiotherapy resistance and its interactions with the tumor environment will help improve cancer responses to radiotherapy. Our review provides a foundation to identify and overcome the obstacles to effective radiotherapy.

Auxin inhibits lignin and cellulose biosynthesis in stone cells of pear fruit via the PbrARF13-PbrNSC-PbrMYB132 transcriptional regulatory cascade.

Stone cells are often present in pear fruit, and they can seriously affect the fruit quality when present in large numbers. The plant growth regulator NAA, a synthetic auxin, is known to play an active role in fruit development regulation. However, the genetic mechanisms of NAA regulation of stone cell formation are still unclear. Here, we demonstrated that exogenous application of 200 µM NAA reduced stone cell content and also significantly decreased the expression level of PbrNSC encoding a transcriptional regulator. PbrNSC was shown to bind to an auxin response factor, PbrARF13. Overexpression of PbrARF13 decreased stone cell content in pear fruit and secondary cell wall (SCW) thickness in transgenic Arabidopsis plants. In contrast, knocking down PbrARF13 expression using virus-induced gene silencing had the opposite effect. PbrARF13 was subsequently shown to inhibit PbrNSC expression by directly binding to its promoter, and further to reduce stone cell content. Furthermore, PbrNSC was identified as a positive regulator of PbrMYB132 through analyses of co-expression network of stone cell formation-related genes. PbrMYB132 activated the expression of gene encoding cellulose synthase (PbrCESA4b/7a/8a) and lignin laccase (PbrLAC5) binding to their promotors. As expected, overexpression or knockdown of PbrMYB132 increased or decreased stone cell content in pear fruit and SCW thickness in Arabidopsis transgenic plants. In conclusion, our study shows that the 'PbrARF13-PbrNSC-PbrMYB132' regulatory cascade mediates the biosynthesis of lignin and cellulose in stone cells of pear fruit in response to auxin signals and also provides new insights into plant SCW formation.

A novel DNA-quantum dot nanostructure electrochemiluminescence aptamer sensor by chain reaction amplification for rapid detection of trace Cd2.

This work proposes a new enzyme-free electrochemiluminescence (ECL) sensing platform based on a novel DNA-quantum dot (QD) nanostructure and hybridization chain reaction (HCR) amplification for the trace detection of Cd2+. First, the Cd2+ aptamer triggers the HCR amplification circuit, so abundant biotin-labeled DNAs are introduced to the electrode, and then biotin as a linker specifically captures a large number of streptavidin (SA)-CdS QD complexes, showing very high ECL signals. After the present Cd2+ binds to its aptamer on the electrode, it causes the linear DNA structure loaded with a large number of QDs to break away from the electrode, resulting in a significantly decreased ECL response. This method combines the HCR-amplified DNA structure-QD signal with the specificity of the biotin-avidin reaction, enabling the rapid detection of Cd2+ in complex water. Therefore, this sensor provides a novel and competitive strategy for detecting heavy metal ions in actual samples, which extends its application to practical settings, such as environmental monitoring and biomedical diagnostics.

Identification of Key Inflammation-related Genes as Potential Diagnostic Biomarkers of Sepsis.

Context: Sepsis is one of the leading causes of mortality for patients with severe infections who had been admitted to intensive care units (ICUs). Early diagnosis, accurate treatment, and management of sepsis remain extremely difficult in clinical settings, due to a lack of early biomarkers and diverse clinical manifestations. Objective: The study intended to identify the key genes and pathways associated with inflammation in sepsis-using microarray technology combined with bioinformatics and key inflammation-related genes (IRGs)-to perform an enrichment analysis and evaluate the value of those genes for the diagnosis and evaluation of prognosis for patients with sepsis. Design: The research team performed a genetic analysis. Setting: The study took place at the Center for Emergency and Critical Medicine at Jinshan Hospital of Fudan University in Jinshan District, Shanghai, China. Groups: The research team created two groups, the sepsis group, individuals with sepsis, and the control group, individuals without sepsis, using data for those groups from five microarray datasets obtained from the Gene Expression Omnibus (GEO) database. Outcome Measures: The research team: (1) downloaded the GSE57065, GSE28750, GSE9692, GSE13904, and GSE54514 datasets from the Gene Expression Omnibus (GEO) database for analysis; (2) analyzed the GSE57065, GSE28750, and GSE9692 datasets to detect the differentially expressed genes (DEGs) in the sepsis and control groups; (3) used Venn diagrams to obtain the intersection of DEGs and inflammation-related genes (IRGs); (4) mapped the protein-protein interaction (PPI) network using the Search Tool for Retrieval of Interacting Genes (STRING) database; (5) detected the hub genes using Cytoscape and cytoHubba; (6) performed an enrichment analysis of hub IRGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG); (7) validated the expression of hub IRGs in sepsis using the GSE13904 dataset; and (8) performed a survival analysis in sepsis using the GSE54514 dataset to explore the prognostic value of the hub IRGs. Results: The research team: (1) identified 104 upregulated DEGs and 4 downregulated DEGs; (2) after defining the intersection of DEGs and IRGs, detected nine differentially expressed IRGs (DEIRGs); and (3) identified five IRGs- haptoglobin (HP), high affinity immunoglobulin gamma Fc receptor I (FCGR1A), cluster of differentiation 163 (CD163), complement C3a receptor 1 human (C3AR1), C-type lectin domain containing 5A (CLEC5A)-that overlapped DEIRGs. The GO and KEGG pathway analyses showed that the hub IRGs became enriched during acute-phase response, acute inflammatory response, specific granule, specific granule membrane, endocytic vesicle membrane, tertiary granule, immunoglobulin G (IgG) binding, complement receptor activity, Ig binding, scavenger receptor activity, and scaffold protein binding. The DEGs also played a significant role in Staphylococcus aureus (S. aureus) infection. The ROC curves showed that HP (AUC: 0.956, 95% CI: 0.924-0.988); FCGR1A (AUC: 0.895,95% CI: 0.827-0.963); CD163 (AUC: 0.838, 95% CI: 0.774-0.901); C3AR1 (AUC: 0.953, 95% CI: 0.913-0.993); and CLEC5A (AUC: 0.951, 95% CI: 0 920-0 981) had meaningful diagnostic value for sepsis. Survival analysis showed that the sepsis and control groups had significant differences in HP (P = .043) and CLEC5A (P < .001). Conclusions: HP, FCGR1A, CD163, C3AR1, and CLEC5A have value for clinical application. Clinicians can use them as diagnostic biomarkers, and they provide research direction for treatment targets for sepsis.

Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii.

Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.

Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity.

BACKGROUND: The mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes. RESULTS: Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process. CONCLUSIONS: This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships.

Luminescent Properties and Charge Compensator Effects of SrMo0.5W0.5O4:Eu3+ for White Light LEDs.

The high-temperature solid-phase approach was used to synthesize Eu3+-doped SrMo0.5W0.5O4 phosphors, whose morphological structure and luminescence properties were then characterized by XRD, SEM, FT-IR, excitation spectra, emission spectra, and fluorescence decay curves. The results reveal that the best phosphor synthesis temperature was 900 °C and that the doping of Eu3+ and charge compensators (K+, Li+, Na+, NH4+) had no effect on the crystal phase change. SrMo0.5W0.5O4:Eu3+ has major excitation peaks at 273 nm, 397 nm, and 464 nm, and a main emission peak at 615 nm, making it a potential red fluorescent material to be used as a down converter in UV LEDs (273 nm and 397 nm) and blue light LEDs (464 nm) to achieve Red emission. The emission spectra of Sr1-yMo0.5W0.5O4:yEu3+(y = 0.005, 0.01, 0.02, 0.05, 0.07) excited at 273 were depicted, with the Eu3+ concentration increasing the luminescence intensity first increases and then decreases, the emission peak intensity of SrMo0.5W0.5O4:Eu3+ achieves its maximum when the doping concentration of Eu3+ is 1%, and the critical transfer distance is calculated as 25.57 Å. When various charge compensators such as K+, Li+, Na+, and NH4+ are added to SrMo0.5W0.5O4:Eu3+, the NH4+ shows the best effect with the optimal doping concentration of 3wt%. The SrMo0.5W0.5O4:Eu3+,NH4+ color coordinate is (0.656,0.343), which is close to that of the ideal red light (0.670,0.333).

Ribosome Biogenesis Regulator 1 Homolog (RRS1) Promotes Cisplatin Resistance by Regulating AEG-1 Abundance in Breast Cancer Cells.

Many ribosomal proteins are highly expressed in tumors and are closely related to their diagnosis, prognosis and pathological characteristics. However, few studies are available on the correlation between ribosomal proteins and chemoresistance. RRS1 (human regulator of ribosome synthesis 1), a critical nuclear protein involved in ribosome biogenesis, also plays a key role in the genesis and development of breast cancer by protecting cancer cells from apoptosis. Given that apoptosis resistance is one of the causes of the cisplatin resistance of tumor cells, our aim was to determine the relationship between RRS1 and cisplatin resistance in breast cancer cells. Here, we report that RRS1 is associated with cisplatin resistance in breast cancer cells. RRS1 silencing increased the sensitivity of MCF-7/DDP cells to cisplatin and inhibited cancer cell proliferation by blocking cell cycle distribution and enhancing apoptosis. AEG-1 (astrocyte elevated gene-1) promotes drug resistance by interfering with the ubiquitination and proteasomal degradation of MDR1 (multidrug resistance gene 1), thereby enhancing drug efflux. We found that RRS1 binds to and stabilizes AEG-1 by inhibiting ubiquitination and subsequent proteasomal degradation, which then promotes drug efflux by upregulating MDR1. Furthermore, RRS1 also induces apoptosis resistance in breast cancer cells through the ERK/Bcl-2/BAX signaling pathway. Our study is the first to show that RRS1 sensitizes breast cancer cells to cisplatin by binding to AEG-1, and it provides a theoretical basis to improve the efficacy of cisplatin-based chemotherapy.

Pathogenetic mechanisms of septic cardiomyopathy.

Sepsis is a serious complication after infection, whose further development may lead to multiple organ dysfunction syndrome and so on. It is an important cause of death in critically ill patients who suffered an infection. Sepsis cardiomyopathy is a common complication that exacerbates the prognosis of patients. At present, though the pathogenesis of sepsis cardiomyopathy is not completely clear, in-depth study of the pathogenesis of sepsis cardiomyopathy and the discovery of its potential therapeutic targets may decrease the mortality of sepsis patients and bring clinical benefits. This article reviews mitochondrial dysfunction, mitophagy, oxidation stress, and other mechanisms in sepsis cardiomyopathy.

Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear.

BACKGROUND: Structural variations (SVs) have recently become a topic of great interest in the area of genetic diversity and trait regulation. As genomic sequencing technologies have rapidly advanced, longer reads have been used to identify SVs at high resolution and with increased accuracy. It is important to choose a suitable sequencing platform and appropriate sequencing depth for SV detection in the pear genome. RESULTS: In this study, two types of long reads from sequencing platforms, continuous long reads from Pacific Biosciences (PB-CLR) and long reads from Oxford Nanopore Technologies (ONT), were used to comprehensively analyze and compare SVs in the pear genome. The mapping rate of long reads was higher when the program Minimap2 rather than the other three mapping tools (NGMLR, LRA and Winnowmap2) was used. Three SV detection programs (Sniffles_v2, CuteSV, and Nanovar) were compared, and Nanovar had the highest sensitivity in detecting SVs at low sequencing depth (10-15×). A sequencing depth of 15× was suitable for SV detection in the pear genome using Nanovar. SVs detected by Sniffles_v2 and CuteSV with ONT reads had the high overlap with presence/absence variations (PAVs) in the pear cultivars 'Bartlett' and 'Dangshansuli', both of them with 38% of insertions and 55% of deletions overlapping with PAVs at sequencing depth of 30×. For the ONT sequencing data, over 37,526 SVs spanning ~ 28 Mb were identified by all three software packages for the 'Bartlett' and 'Dangshansuli' genomes. Those SVs were annotated and combined with transcriptome profiles derived from 'Bartlett' and 'Dangshansuli' fruit flesh at 60 days after cross-pollination. Several genes related to levels of sugars, acid, stone cells, and aromatic compounds were identified among the SVs. Transcription factors were then predicted among those genes, and results included bHLH, ERF, and MYB genes. CONCLUSION: SV detection is of great significance in exploring phenotypic differences between pear varieties. Our study provides a framework for assessment of different SV software packages and sequencing platforms that can be applied in other plant genome studies. Based on these analyses, ONT sequencing data was determined to be more suitable than PB-CLR for SV detection in the pear genome. This analysis model will facilitate screening of genes related to agronomic traits in other crops.

Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants.

Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a "barcoding" bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.

Au-quantum dot nanocluster electrochemiluminescence coupled with cycling-amplification for sensitive microRNA detection.

A novel polyamidoamine (PAMAM) dendrimer-Au nanocluster composite was synthesized, and used to fabricate a new amplified electrochemiluminescence (ECL) signal probe for sensitive detection of microRNA by multiple strand displacement amplification (SDA) strategy. The as prepared PAMAM-Au nanocluster with many amino groups could assemble a large number of quantum dots (QDs) to greatly amplify ECL of the probe. In addition, a new sliver nanocluster (NC) with excellent conductivity and many reactive carboxyl groups was prepared, and used to immobilize a large amount of capture (c1) DNA molecules on the electrode. Moreover, by using bifunctional DNA strand displacement reaction-mediated multiple cycling-amplification technique, a small number of target miRNA could induce to generate abundant DNA (t1) fragments, which was used as a linker to hybridize with c1 DNA on the electrode, and then conjugate many amplified QDs probe. Thus an amplified ECL analytical method for detecting target miRNA was designed, and highly sensitive detection of miRNA was achieved. This newly established strategy paves a new way for homogeneous microRNA detection, which hold great potential for application in early clinical diagnosis.

Long non-coding RNA KCNQ1OT1 promotes proliferation, migration and invasion via targeting miR-134 in retinoblastoma.

BACKGROUND: Long non-coding RNAs (lncRNAs) exert a significant role in carcinogenesis. lncRNA KCNQ1OT1 is detected in many tumors and is considered as an oncogene. The expression and mechanism of KCNQ1OT1 in retinoblastoma (Rb) are not clearly elucidated. METHODS: KCNQ1OT1, miR-134 and TRIM44 mRNA expression were examined by a quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Proliferation, migration and invasion of Weri-Rb1 and Y79 cells were tested by cell counting kit-8, colony formation, scratch and transwell assays. Meanwhile, the regulatory relationships among KCNQ1OT1, miR-134 and TRIM44 were clarified by several biological experiments, including dual-luciferase reporter assay, RNA immunoprecipitation, subcellular distribution, qRT-PCR and western blotting. RESULTS: lncRNA KCNQ1OT1 was up-regulated in Rb tissues and Rb cell lines. In addition, the expression of KCNQ1OT1 was negatively correlated with the disease-free survival rate of RB patients. Silencing KCNQ1OT1 could significantly inhibit the RB progression in vivo and in vitro. The analysis of the mechanism of KCNQ1OT1 showed that KCNQ1OT1 can sponge miR-134, and miR-134 may inhibit TRIM44 expression. Moreover, the rescue assays showed that KCNQ1OT1 promoted RB progression by regulating the miR-134/TRIM44 pathway. CONCLUSIONS: The present study indicates that a new KCNQ1OT1/miR-134/TRIM44 pathway regulates Rb progression. It may be used as a potential prognostic marker for Rb.