SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress.

Alternative splicing (AS) regulates gene expression and increases proteomic diversity for the fine tuning of stress responses in plants, but the exact mechanism through which AS functions in plant stress responses is not thoroughly understood. Here, we investigated how AS functions in poplar (Populus trichocarpa), a popular plant for bioremediation, in response to lead (Pb) stress. Using a proteogenomic analysis, we determine that Pb stress induced alterations in AS patterns that are characterized by an increased use of nonconventional splice sites and a higher abundance of Pb-responsive splicing factors (SFs) associated with Pb-responsive transcription factors. A strong Pb(II)-inducible chaperone protein, PtHSP70, that undergoes AS was further characterized. Overexpression of its two spliced isoforms, PtHSP70-AS1 and PtHSP70-AS2, in poplar and Arabidopsis significantly enhances the tolerance to Pb. Further characterization shows that both isoforms can directly bind to Pb(II), and PtHSP70-AS2 exhibits 10-fold higher binding capacities and a greater increase in expression under Pb stress, thereby reducing cellular toxicity through Pb(II) extrusion and conferring Pb tolerance. AS of PtHSP70 is found to be regulated by PtU1-70K, a Pb(II)-inducible core SF involved in 5'-splice site recognition. Because the same splicing pattern is also found in HSP70 orthologs in other plant species, AS of HSP70 may be a common regulatory mechanism to cope with Pb(II) toxicity. Overall, we have revealed a novel post-transcriptional machinery that mediates heavy metal tolerance in diverse plant species. Our findings offer new molecular targets and bioengineering strategies for phytoremediation and provide new insight for future directions in AS research.

Chondroitin sulfate-modified tragacanth gum-gelatin composite nanocapsules loaded with curcumin nanocrystals for the treatment of arthritis.

Rheumatoid arthritis (RA) is a chronic autoimmune disease of yet undetermined etiology that is accompanied by significant oxidative stress, inflammatory responses,  and damage to joint tissues. In this study, we designed chondroitin sulfate (CS)-modified tragacanth gum-gelatin composite nanocapsules (CS-Cur-TGNCs) loaded with curcumin nanocrystals (Cur-NCs), which rely on the ability of CS to target CD44 to accumulate drugs in inflamed joints. Cur was encapsulated in the form of nanocrystals into tragacanth gum-gelatin composite nanocapsules (TGNCs) by using an inborn microcrystallization method, which produced CS-Cur-TGNCs with a particle size of approximately 80 ± 11.54 nm and a drug loading capacity of 54.18 ± 5.17%. In an in vitro drug release assay, CS-Cur-TGNCs showed MMP-2-responsive properties. During the treatment of RA, CS-Cur-TGNCs significantly inhibited oxidative stress, promoted the polarization of M2-type macrophages to M1-type macrophages, and decreased the expression of inflammatory factors (TNF-α, IL-1ß, and IL-6). In addition, it also exerted excellent anti-inflammatory effects, and significantly alleviated the swelling of joints during the treatment of gouty arthritis (GA). Therefore, CS-Cur-TGNCs, as a novel drug delivery system, could lead to new ideas for clinical therapeutic regimens for RA and GA.

The Accurate Imaging of Collective Gold Nanorods with a Polarization-Dependent Dark-Field Light Scattering Microscope.

Anisotropic nanomaterials, such as gold nanorods (AuNRs), could be employed as an orientation platform due to their polarization-dependent surface plasmon resonance. However, a variety of factors would affect the dark-field light scattering imaging of anisotropic nanomaterials, resulting in an unstable signal, which is not advantageous to its further application. In this work, the localized surface plasmon resonance properties of a few AuNRs at different angles were excited by polarization with a conventional dark-field microscope, in which it was found that the ratio of AuNRs' light scattering intensity at different polarization angles (I) to that without a polarizer (I0) reflected the orientation information of AuNRs. Furthermore, the light scattering signal ratio between the parallel polarization (Ip) and that without a polarizer (I0) was closely related with the aspect ratio of AuNRs, which could not be affected by external conditions. To verify this concept, a highly sensitive and selective assay of the alkaline phosphatase activity in human serum was successfully developed based on the chemical etching of AuNRs, resulting in a lower aspect ratio and a lesser Ip/I0. This result holds great promise for polarization-dependent colorimetric nanomaterials and single-particle tracers in living cells.

Two-Dimensional Analysis Method for Highly Sensitive Detection of Dual MicroRNAs in Breast Cancer Cells.

Multiple biomarker detection is crucial for early clinical diagnosis, and it is significant to achieve the simultaneous detection of multiple biomarkers with the same nanomaterial. In this work, the hairpin DNA strands were selectively modified on the surface of gold nanorods (AuNRs) to construct two kinds of nanoprobes by rational design. When in the presence of dual microRNAs, AuNRs were assembled to form end-to-end (ETE) and side-by-side (SBS) dimers. Compared with a single AuNR, the dark-field scattering intensity and red color percentage variation of dimers were extremely distinguished, which could be developed for dual microRNA detection by combining the red color percentage and scattering intensity with the data processing method of principal component analysis to construct a two-dimensional analysis method. Especially, the fraction of AuNR dimers presented a linear relationship with the amount of microRNAs. Based on this, microRNA-21 and microRNA Let-7a in breast cancer cells were detected with the detection limits of 1.72 and 0.53 fM, respectively. This method not only achieved the sensitive detection of dual microRNAs in human serum but also realized the high-resolution intracellular imaging, which developed a new way for the oriented assembly of nanomaterials and biological detection in living cells.

Deficiency in flavonoid biosynthesis genes CHS, CHI, and CHIL alters rice flavonoid and lignin profiles.

Lignin is a complex phenylpropanoid polymer deposited in the secondary cell walls of vascular plants. Unlike most gymnosperm and eudicot lignins that are generated via the polymerization of monolignols, grass lignins additionally incorporate the flavonoid tricin as a natural lignin monomer. The biosynthesis and functions of tricin-integrated lignin (tricin-lignin) in grass cell walls and its effects on the utility of grass biomass remain largely unknown. We herein report a comparative analysis of rice (Oryza sativa) mutants deficient in the early flavonoid biosynthetic genes encoding CHALCONE SYNTHASE (CHS), CHALCONE ISOMERASE (CHI), and CHI-LIKE (CHIL), with an emphasis on the analyses of disrupted tricin-lignin formation and the concurrent changes in lignin profiles and cell wall digestibility. All examined CHS-, CHI-, and CHIL-deficient rice mutants were largely depleted of extractable flavones, including tricin, and nearly devoid of tricin-lignin in the cell walls, supporting the crucial roles of CHS and CHI as committed enzymes and CHIL as a noncatalytic enhancer in the conserved biosynthetic pathway leading to flavone and tricin-lignin formation. In-depth cell wall structural analyses further indicated that lignin content and composition, including the monolignol-derived units, were differentially altered in the mutants. However, regardless of the extent of the lignin alterations, cell wall saccharification efficiencies of all tested rice mutants were similar to that of the wild-type controls. Together with earlier studies on other tricin-depleted grass mutant and transgenic plants, our results reflect the complexity in the metabolic consequences of tricin pathway perturbations and the relationships between lignin profiles and cell wall properties.

Vacuum-assisted dedusting lithotripsy in the treatment of kidney and proximal ureteral stones less than 3 cm in size.

PURPOSE: This study aimed to compare the outcomes of vacuum-assisted dedusting lithotripsy (VADL) using flexible vacuum-assisted ureteral access sheath (FV-UAS) versus traditional flexible ureteroscopic lithotripsy (fURL) in patients with kidney or proximal ureteral calculi less than 3 cm in size. METHODS: A total of 371 patients who successfully underwent fURL treatment were enrolled. These patients were divided into traditional fURL group and VADL group. Outcomes of both groups were compared using 1:1 propensity score-matched analysis. Stratified analyses based on stone size and location were also conducted. RESULTS: Finally, 103 well-matched patients in each group were identified. No septic shock or death occurred. The immediate stone-free rate (SFR) and follow-up SFR of VADL group were significantly higher (78.6% vs. 50.5%, p < 0.001; 94.2%% vs. 75.7%, p < 0.001). No difference was observed in postoperative fever rate (2.9% vs. 3.9%, p = 1.000) and duration of lithotripsy (37.7 ± 20.1 min vs. 40.3 ± 18.9 min, p = 0.235). For patients with stones ≤ 2 cm in size, the immediate SFR and follow-up SFR in VADL group were higher (86.7% vs. 60.6%, p < 0.001; 96.0% vs. 83.1%, p = 0.010). The same trend was observed in the 2-3 cm subgroup (57.1% vs. 28.1%, p = 0.023; 89.3% vs. 59.4%, p = 0.009). Although the in situ fragmentation strategy was employed more frequently in VADL group for lower pole stones, the SFR was still higher. Subgroup analyses did not reveal any significant differences in either infectious complications or duration of lithotripsy. CONCLUSION: VADL technique can significantly improve the postoperative SFR for the patients with kidney or proximal ureteral stones less than 3 cm in size treated by flexible ureteroscope.

Prevalence of psychological distress among people living with HIV/AIDS: a systematic review and meta-analysis.

Although people living with HIV/AIDS (PLWHA) are known to be vulnerable to psychological distress (PD), little is known about the prevalence of PD among PLWHA. A systematic literature search of several databases was conducted from inception to August 2021 focusing on studies reporting on PD symptoms among PLWHA. The overall prevalence estimates were pooled using a random-effects meta-analysis. Differences according to study-level characteristics were examined using stratified meta-analysis. We pooled and analyzed data from 15 studies comprising 5593 PLWHA. The prevalence rate of PD among PLWHA was 43.7% (95% Confidence Interval: 29.9-57.5%). Subgroup analyses by gender, country, CD4 count, employment status and ever attended school found no statistically significant differences in the prevalence of PD. Heterogeneity in the prevalence of PD among PLWHA was partially explained by the assessment tool. Further large-scale studies of high quality are warranted to identify risk factors of PD in PLWHA in their respective socio-cultural contexts.

Health Risk Assessment of Organophosphate Flame Retardants in Soil Across China Based on Monte Carlo Simulation.

Health risks from exposure to contaminants are generally estimated by evaluating concentrations of the contaminants in environmental matrixes. However, accurate health risk assessment is difficult because of uncertainties regarding exposures. This study aims to utilize data on the concentrations of organophosphate flame retardants (OPFRs) in surface soil across China coupled with Monte Carlo simulations to compensate for uncertainties in exposure to evaluate the health risks associated with contamination of soil with this class of flame retardants. Results revealed that concentrations of ∑OPFRs were 0.793-406 ng/g dry weight (dw) with an average of 23.2 ng/g dw. In terms of spatial distribution, higher OPFRs concentrations were found in economically developed regions. Although the values of health risk of OPFRs in soil across China were below the threshold, the high concentrations of OPFRs in soil in some regions should attract more attentions in future. Sensitivity analysis revealed that concentrations of OPFRs in soil, skin adherence factor, and exposure duration were the most sensitive parameters in health risk assessment. In summary, the study indicated that the national scale soil measurement could provide unique information on OPFRs exposure and health risk assessment, which was useful for the management of soil in China and for better understanding of the environmental fate of OPFRs in the global perspective.

Probiotics-Fermented Grifola frondosa Total Active Components: Better Antioxidation and Microflora Regulation for Alleviating Alcoholic Liver Damage in Mice.

Alcoholic liver damage is caused by long-term drinking, and it further develops into alcoholic liver diseases. In this study, we prepared a probiotic fermentation product of Grifola frondosa total active components (PFGF) by fermentation with Lactobacillus acidophilus, Lactobacillus rhamnosus, and Pediococcus acidilactici. After fermentation, the total sugar and protein content in the PFGF significantly decreased, while the lactic acid level and antioxidant activity of the PFGF increased. Afterward, we investigated the alleviating effect of PFGF on alcoholic liver injury in alcohol-fed mice. The results showed that the PFGF intervention reduced the necrosis of the liver cells, attenuated the inflammation of the liver and intestines, restored the liver function, increased the antioxidant factors of the liver, and maintained the cecum tissue barrier. Additionally, the results of the 16S rRNA sequencing analysis indicated that the PFGF intervention increased the relative abundance of beneficial bacteria, such as Lactobacillus, Ruminococcaceae, Parabacteroids, Parasutterella, and Alistipes, to attenuate intestinal inflammation. These results demonstrate that PFGF can potentially alleviate alcoholic liver damage by restoring the intestinal barrier and regulating the intestinal microflora.

Polycyclic Aromatic Hydrocarbons in the Marine Atmosphere from the Western Pacific to the Southern Ocean: Spatial Variability, Gas/Particle Partitioning, and Source Apportionment.

The spatial variability of polycyclic aromatic hydrocarbons (PAHs) in the marine atmosphere contributes to the understanding of the global sources, fate, and impact of this contaminant. Few studies conducted to measure PAHs in the oceanic atmosphere have covered a large scale, especially in the Southern Ocean. In this study, high-volume air samples were taken along a cross-section from China to Antarctica and analyzed for gaseous and particulate PAHs. The data revealed the spatial distribution, gas-particle partitioning, and source contributions of PAHs in the Pacific, Indian, and Southern Oceans. The median concentration (gaseous + particulate) of ∑24PAHs was 3900 pg/m3 in the Pacific Ocean, 2000 pg/m3 in the Indian Ocean, and 1200 pg/m3 in the Southern Ocean. A clear latitudinal gradient was observed for airborne PAHs from the western Pacific to the Southern Ocean. Back trajectories (BTs) analysis showed that air masses predominantly originated from populated land had significantly higher concentrations of PAHs than those from the oceans or Antarctic continents/islands. The air mass origins and temperature have significant influences on the gas-particle partitioning of PAHs. Source analysis by positive matrix factorization (PMF) showed that the highest contribution to PAHs was from coal combustion emissions (52%), followed by engine combustion emissions (27%) and wood combustion emissions (21%). A higher contribution of PAHs from wood combustion was found in the eastern coastal region of Australia. In contrast, engine combustion emissions primarily influenced the sites in Southeast Asia.

Development of an Escherichia coli whole cell biocatalyst for the production of hyperoside.

OBJECTIVE: To produce high concentrations of hyperoside from quercetin using recombinant Escherichia coli with in situ regeneration of UDP-galactose. RESULTS: Sucrose synthase from Glycine max (GmSUS) was co-expressed with UDP-glucose epimerase from E. coli (GalE) in E. coli for regenerating UDP-galactose from UDP and sucrose. Glycosyltransferase from Petunia hybrida (PhUGT) was introduced to synthesize hyperoside from quercetin through the regeneration system of UDP-galactose. Co-expressing with molecular chaperones GroEL/ES successfully enhanced the catalytic efficiency of the recombinant strain, which assisted the soluble expression of PhUGT. By using a fed-batch approach, the production of hyperoside reached 863.7 mg L-1 with a corresponding molar conversion of 93.6% and a specific productivity of 72.5 mg L-1 h-1. CONCLUSION: The method described herein for hyperoside production can be widely applied for the synthesis of isorhamnetin-3-O-galactoside, kaempferol-3-O-galactoside and other flavonoids.

Sensitivity of Colletotrichum nymphaeae to Six Fungicides and Characterization of Fludioxonil-Resistant Isolates in China.

Colletotrichum nymphaeae is the dominant species causing anthracnose disease of peach in China. In this study, 140 isolates of C. nymphaeae were assessed for their sensitivity to six fungicides. It was found that C. nymphaeae was highly resistant to carbendazim, procymidone, and boscalid but sensitive to pyraclostrobin and prochloraz. For fludioxonil, the fungus exhibited differential sensitivities (i.e., approximately 14% of isolates were resistant to fludioxonil and the resistance was stable). Fludioxonil-resistant isolates had a mean EC50 value of 2.2380 µg/ml, whereas the mean EC50 value was 0.0194 µg/ml in fludioxonil-sensitive isolates. The mean EC50 values of C. nymphaeae for pyraclostrobin and prochloraz were 0.0083 µg/ml and 0.002 µg/ml, respectively. No cross-resistance was observed between fungicides from different groups. Mycelial growth rate, control efficacy, and osmotic stress responses were significantly different (P < 0.05) between fludioxonil-sensitive (FluS) and -resistant (FluR) isolates, but no significant difference was observed (P > 0.05) in virulence and sporulation between FluS and FluR isolates. No mutation was detected in coding regions of the CnOs-1, Cal, Hk1, Hog1, TPI, and Mrr1 genes. Interestingly, with fludioxonil treatment, the expression of ABC transporter gene atrB was significantly overexpressed in some resistant isolates. However, overexpression of the atrB gene was not detected in one moderately and one highly resistant isolate, indicating that other unknown mechanisms may be involved. Current findings uncovered several effective chemicals and provided the foundation for designing management strategies to practically control peach anthracnose with the most effective demethylation inhibitor fungicides and quinone outside inhibitor fungicides.

An Improved MobileNet Network with Wavelet Energy and Global Average Pooling for Rotating Machinery Fault Diagnosis.

In recent years, neural networks have shown good performance in terms of accuracy and efficiency. However, along with the continuous improvement in diagnostic accuracy, the number of parameters in the network is increasing and the models can often only be run in servers with high computing power. Embedded devices are widely used in on-site monitoring and fault diagnosis. However, due to the limitation of hardware resources, it is difficult to effectively deploy complex models trained by deep learning, which limits the application of deep learning methods in engineering practice. To address this problem, this article carries out research on network lightweight and performance optimization based on the MobileNet network. The network structure is modified to make it directly suitable for one-dimensional signal processing. The wavelet convolution is introduced into the convolution structure to enhance the feature extraction ability and robustness of the model. The excessive number of network parameters is a challenge for the deployment of networks and also for the running performance problems. This article analyzes the influence of the full connection layer size on the total network. A network parameter reduction method is proposed based on GAP to reduce the network parameters. Experiments on gears and bearings show that the proposed method can achieve more than 97% classification accuracy under the strong noise interference of -6 dB, showing good anti-noise performance. In terms of performance, the network proposed in this article has only one-tenth of the number of parameters and one-third of the running time of standard networks. The method proposed in this article provides a good reference for the deployment of deep learning intelligent diagnosis methods in embedded node systems.

Alternative Splicing and Its Roles in Plant Metabolism.

Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.

Temporal Trend of Polycyclic Aromatic Hydrocarbons in Atmosphere: A Case Study within 24 h after Snowfall.

Based on air samples within 24 h after snowfall, gaseous and particulate concentrations of 16 priority PAHs were obtained, which provided a good opportunity to study the temporal trend of atmospheric PAHs. An obvious temporal trend with atmospheric concentration was observed, which was mainly influenced by emission sources. It was found that the maximum concentration (Σ16PAHs) was 272.8 ng/m3, appeared in the rush hour of traffic. To the contrary, the minimum concentration was 82.39 ng/m3 at the period with the least anthropogenic activities. The values of particle-phase fraction[Formula: see text]) and G/P partitioning quotient (log K P) were increased along with molecular weight of PAHs. However, for individual PAHs, the differences with [Formula: see text] and log K P were not obvious within 24 h. Furthermore, similar statistically significant positive correlations were found between log K P and log K OA among different periods. According to the short sampling program, chemical properties should be the major influencing factor for the temporal trend of G/P partitioning. The results of the case study provided new insights into the research field of G/P partitioning of PAHs.

Effects of IL-18 on the proliferation and steroidogenesis of bovine theca cells: Possible roles in the pathogenesis of polycystic ovary syndrome.

Interleukin 18 (IL-18) is a pleiotropic pro-inflammatory cytokine and is associated with arrested follicle development and anovulation which are the typical pathological changes of PCOS. Theca cells (TCs) have a key role in follicular growth and atresia. But whether IL-18 can directly affect ovarian TCs function is unknown. Therefore, the objective of this study was to determine the effect of IL-18 on proliferation and steroidogenesis of bovine TCs and to explore the biological effect of IL-18 on folliculogenesis. This work revealed that at 300-1000 pg/mL, IL-18 led to a time- and dose-dependently increase in cell proliferation (P < .05). IL-18 increased 17-hydroxyprogesterone (17OHP4) and androstenedione (A2) secretion with up-regulation of key steroidogenesis-related genes CYP11A1 and CYP17A1 (P < .05). Furthermore, our data demonstrated that the IL-18R protein is predominantly expressed in small-follicle (3-6 mm) TCs than large follicles (8-22 mm) by immunohistochemistry. We also found that the stimulation effects of IL-18 on TCs can be reversed with the addition of IL-18BP as early as at 4 hours of culture and reached the peak at 16 hours. We conclude that IL-18 appears to target TCs in bovine, and suggest an important role for this cytokine in ovarian function. Present findings further validate potential effects of IL-18 in the conditions associated with follicular dysplasia and excessive growth of ovarian TCs (such as PCOS). But additional research is needed to further understand the mechanism of action of IL-18 in theca cells as well as its precise role in folliculogenesis.

Phylogenetic comparison of 5' splice site determination in central spliceosomal proteins of the U1-70K gene family, in response to developmental cues and stress conditions.

Intron-containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding the eukaryotic transcriptome and proteome. In eukaryotic cells, precursor mRNA (pre-mRNA) splicing is performed by a mega-macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5'-splice site recognition. Its central component, named U1-70K, has been extensively characterized in animals and yeast. Very few investigations on U1-70K genes have been conducted in plants, however. To this end, we performed a comprehensive study to systematically identify 115 U1-70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that the expansion of the plant U1-70K gene family was likely to have been driven by whole-genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1-70Ks are likely to preserve their conserved molecular function across plant lineages and play an important functional role in response to environmental stresses. Furthermore, genetic analysis using T-DNA insertion mutants suggested that Arabidopsis U1-70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source for future mechanistic studies on this U1 snRNP-specific splicing factor.

SWATH-MS based quantitive proteomics reveal regulatory metabolism and networks of androdioecy breeding system in Osmanthus fragrans.

BACKGROUND: The fragrant flower plant Osmanthus fragrans has an extremely rare androdioecious breeding system displaying the occurrence of males and hermaphrodites in a single population, which occupies a crucial intermediate stage in the evolutionary transition between hermaphroditism and dioecy. However, the molecular mechanism of androdioecy plant is very limited and still largely unknown. RESULTS: Here, we used SWATH-MS-based quantitative approach to study the proteome changes between male and hermaphroditic O. fragrans pistils. A total of 428 proteins of diverse functions were determined to show significant abundance changes including 210 up-regulated and 218 down-regulated proteins in male compared to hermaphroditic pistils. Functional categorization revealed that the differentially expressed proteins (DEPs) primarily distributed in the carbohydrate metabolism, secondary metabolism as well as signaling cascades. Further experimental analysis showed the substantial carbohydrates accumulation associated with promoted net photosynthetic rate and water use efficiency were observed in purplish red pedicel of hermaphroditic flower compared with green pedicel of male flower, implicating glucose metabolism serves as nutritional modulator for the differentiation of male and hermaphroditic flower. Meanwhile, the entire upregulation of secondary metabolism including flavonoids, isoprenoids and lignins seem to protect and maintain the male function in male flowers, well explaining important feature of androdioecy that aborted pistil of a male flower still has a male function. Furthermore, nine selected DEPs were validated via gene expression analysis, suggesting an extra layer of post-transcriptional regulation occurs during O. fragrans floral development. CONCLUSION: Taken together, our findings represent the first SWATH-MS-based proteomic report in androdioecy plant O. fragrans, which reveal carbohydrate metabolism, secondary metabolism and post-transcriptional regulation contributing to the androdioecy breeding system and ultimately extend our understanding on genetic basis as well as the industrialization development of O. fragrans.

Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice.

BACKGROUND: Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established. RESULTS: In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism. CONCLUSIONS: Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.

Rice (Oryza sativa) molecular breeding has gained considerable attention in recent years, but inaccurate genome annotation hampers its progress and functional studies of the rice genome. In this study, we applied single-molecule long-read RNA sequencing (lrRNA_seq)-based proteogenomics to reveal the complexity of the rice transcriptome and its coding abilities. Surprisingly, approximately 60% of loci identified by lrRNA_seq are associated with natural antisense transcripts (NATs). The high-density genomic arrangement of NAT genes suggests their potential roles in the multifaceted control of gene expression. In addition, a large number of fusion and intergenic transcripts have been observed. Furthermore, 906,456 transcript isoforms were identified, and 72.9% of the genes can generate splicing isoforms. A total of 706,075 posttranscriptional events were subsequently categorized into 10 subtypes, demonstrating the interdependence of posttranscriptional mechanisms that contribute to transcriptome diversity. Parallel short-read RNA sequencing indicated that lrRNA_seq has a superior capacity for the identification of longer transcripts. In addition, over 190,000 unique peptides belonging to 9,706 proteoforms/protein groups were identified, expanding the diversity of the rice proteome. Our findings indicate that the genome organization, transcriptome diversity, and coding potential of the rice transcriptome are far more complex than previously anticipated.