Search Results (361)

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as MYBs, bHLHs, and WD40s. LncRNAs can target these ripening-related genes to form regulatory modules, incorporated into the sweet cherry fruit ripening regulatory network. Our study reveals that the lncRNA-mRNA module is an important component of the sweet cherry fruit ripening regulatory network. During sweet cherry fruit ripening, the differential expression of lncRNAs will meditate the spatio-temporal specific expression of ripening-related target genes (encoding enzymes and transcription factors related to ABA metabolism, cell wall metabolism and anthocyanin metabolism), thus driving fruit ripening. Full article

Inherited retinal degenerations (IRDs) are a group of genetic disorders characterized by the progressive degeneration of retinal cells, leading to irreversible vision loss. SLC4A7 has emerged as a candidate gene associated with IRDs, yet its mechanisms remain largely unknown. This study aims to investigate the role of slc4a7 in retinal development and its associated molecular pathogenesis in zebrafish. Morpholino oligonucleotide knockdown, CRISPR/Cas9 genome editing, quantitative RT-PCR, eye morphometric measurements, immunofluorescent staining, TUNEL assays, visual motor responses, optokinetic responses, rescue experiments, and bulk RNA sequencing were used to assess the impact of slc4a7 deficiency on retinal development. Our results demonstrated that the knockdown of slc4a7 resulted in a dose-dependent reduction in eye axial length, ocular area, and eye-to-body-length ratio. The fluorescence observations showed a significant decrease in immunofluorescence signals from photoreceptors and in mCherry fluorescence from RPE in slc4a7-silenced morphants. TUNEL staining uncovered the extensive apoptosis of retinal cells induced by slc4a7 knockdown. Visual behaviors were significantly impaired in the slc4a7-deficient larvae. GO and KEGG pathway analyses reveal that differentially expressed genes are predominantly linked to aspects of vision, ion channels, and phototransduction. This study demonstrates that the loss of slc4a7 in larvae led to profound visual impairments, providing additional insights into the genetic mechanisms predisposing individuals to IRDs caused by SLC4A7 deficiency. Full article

Intervertebral disc disease (IDD) is a debilitating spine condition that can be caused by intervertebral disc (IVD) damage which progresses towards IVD degeneration and dysfunction. Recently, human pluripotent stem cells (hPSCs) were recognized as a valuable resource for cell-based regenerative medicine in skeletal diseases. Therefore, adult somatic cells reprogrammed into human induced pluripotent stem cells (hiPSCs) represent an attractive cell source for the derivation of notochordal-like cells (NCs) as a first step towards the development of a regenerative therapy for IDD. Utilizing a differentiation method involving treatment with a four-factor cocktail targeting the BMP, FGF, retinoic acid, and Wnt signaling pathways, we differentiate CRISPR/Cas9-generated mCherry-reporter knock-in hiPSCs into notochordal-like cells. Comprehensive analysis of transcriptomic changes throughout the differentiation process identified regulation of histone methylation as a pivotal driver facilitating the differentiation of hiPSCs into notochordal-like cells. We further provide evidence that specific inhibition of histone demethylases KDM2A and KDM7A/B enhanced the lineage commitment of hiPSCs towards notochordal-like cells. Our results suggest that inhibition of KDMs could be leveraged to alter the epigenetic landscape of hiPSCs to control notochord-specific gene expression. Thus, our study highlights the importance of epigenetic regulators in stem cell-based regenerative approaches for the treatment of disc degeneration. Full article

The insular cortex is an important hub for sensory and emotional integration. It is one of the areas consistently found activated during pain. While the insular’s connections to the limbic system might play a role in the aversive and emotional component of pain, its connections to the descending pain system might be involved in pain intensity coding. Here, we used anterograde tracing with viral expression of mCherry fluorescent protein, to examine the connectivity of insular axons to different brainstem nuclei involved in the descending modulation of pain in detail. We found extensive connections to the main areas of descending pain control, namely, the periaqueductal gray (PAG) and the raphe magnus (RMg). In addition, we also identified an extensive insular connection to the parabrachial nucleus (PBN). Although not as extensive, we found a consistent axonal input from the insula to different noradrenergic nuclei, the locus coeruleus (LC), the subcoereuleus (SubCD) and the A5 nucleus. These connections emphasize a prominent relation of the insula with the descending pain modulatory system, which reveals an important role of the insula in pain processing through descending pathways. Full article

In this study, a zein-stabilized lemon essential oil Pickering emulsion (ZLPE) was incorporated into a carboxymethyl cellulose/gelatin (CMC/GL) composite film to develop a bio-based packaging material with bioactive properties. The average droplet size of the ZLPE was measured at 3.62 ± 0.08 μm, with a zeta potential of −31.33 ± 0.32 mV, highlighting its excellent stability. The image results of confocal laser microscopy and scanning electron microscopy validated the uniform distribution of ZLPE in the film. The incorporation of ZLPE reduced the water solubility of films by 45.90% and decreased its water vapor permeability by 22.61%, thereby enhancing its hydrophobicity. Additionally, the ZLPE-loaded film improved mechanical properties, enhanced UV-blocking capabilities, and increased thermal stability. The introduction of ZLPE led to the antioxidant activity of the CMC/GL film increasing by six times the original level and endowed it with outstanding antibacterial properties. As a result, cherries packaged with the ZLPE film demonstrated superior preservation performance and extended shelf life in the preservation experiment, exhibiting the film’s potential as a food packaging material. Full article

Instant Cascara (IC) is a sustainable beverage made from dried coffee cherry pulp, a by-product of coffee processing. It is rich in nutrients and bioactive compounds and has a high concentration of antioxidants. This study explored the impact of regular IC consumption on colonic motor function and innervation. Over a period of 4 weeks, male and female healthy rats were given drinking water containing 10 mg/mL of IC. Thereafter, colon samples were obtained to evaluate the longitudinal (LM) and circular (CM) smooth muscle contractile response to acetylcholine (ACh) and electrical field stimulation (EFS) in an organ bath, before and after atropine administration (10⁻⁶ M). Histological and immunohistochemical analyses assessed colon damage, muscle thickness, and immunoreactivity to substance P (SP) and neuronal nitric oxide synthase (nNOS). ACh and EFS induced similar responses across groups, but the CM response to EFS was greater in females compared with males, despite their lower body weight. Atropine completely blocked the response to ACh but only partially antagonized the neural response to EFS, particularly that of CM in females treated with IC, which had a greater liquid intake than those exposed to water. However, in the myenteric ganglia, no statistically significant differences were observed in SP or nNOS. Our results suggest that regular IC exposure may enhance specific neural pathway functions, particularly in females, possibly due to their increased IC consumption. Full article

This study evaluates the fermentation performances of non-Saccharomyces strains in fermenting cherry must from Italian cherries unsuitable for selling and not intended to be consumed fresh, and their effects on the chemical composition of the resulting wine. Fermentation trials in 100 and 500 mL of must were carried out to select 21 strains belonging to 11 non-Saccharomyces species. Cherry wines obtained by six select strains were chemically analyzed for fixed and volatile compounds. Quantitative data were statistically analyzed by agglomerative hierarchical clustering, partial least squared discriminant analysis, and principal component analysis. Wines revealed significant differences in their composition. Lactic acid and phenylethyl acetate levels were very high in wines produced by Lachancea and Hanseniaspora, respectively. Compared to S. cerevisiae wine, non-Saccharomyces wines had a lower content of fatty acid ethyl esters 4-vinyl guaiacol and 4-vinyl phenol. The multivariate analysis discriminated between wines, demonstrating the different contributions of each strain to aroma components. Specifically, all wines from non-Saccharomyces strains were kept strictly separate from the control wine. This study provided comprehensive characterization traits for non-conventional strains that enhance the aroma complexity of cherry-based wine. The use of these yeasts in cherry wine production appears promising. Further investigation is required to ascertain their suitability for larger-scale fermentation. Full article

Leaf spot, a major apple disease, manifests in diverse symptoms. In this study, the pathogen was isolated from diseased ‘Yanfu 3’ apple leaves in Yantai, Shandong Province, and identified as Neopestalotiopsis clavispora through morphological observation, molecular identification, and multi-gene (ITS, TEF1α, and TUB2) phylogenetic analysis. Three isolates (YTNK01, YTNK02, and YTNK03) were selected for pathogenicity tests to verify Koch’s postulates. To our knowledge, this is the first report of N. clavispora being responsible for apple leaf spots in China, and the disease has been named ‘apple Neopestalotiopsis leaf spot’. Additionally, N. clavispora was found to infect crabapple, sweet cherry, grape, peach, and pear under laboratory conditions, indicating that these fruit trees may be potential hosts for N. clavispora in the field. The in vitro toxicity of ten fungicides to the pathogen was assessed using the mycelial growth rate method. All ten fungicides were effective in inhibiting the growth of N. clavispora. Among them, those based on pylocyanonitrile, propiconazole, pyraclostrobin, tebuconazole, diphenoxazole, and osthole showed higher toxicity to N. clavispora, with EC₅₀ values of 0.11, 0.41, 0.47, 1.32, 1.85, and 3.82 µg/mL, respectively. These fungicides could be used as alternatives to prevent this disease in production. Overall, these findings provide valuable insights into the characteristics of N. clavispora causing apple leaf spot and are crucial for developing effective management strategies. Full article

The measurement of dynamic changes in protein level and localization throughout the cell cycle is of major relevance to studies of cellular processes tightly coordinated with the cycle, such as replication, transcription, DNA repair, and checkpoint control. Currently available methods include biochemical assays of cells in bulk following synchronization, which determine protein levels with poor temporal and no spatial resolution. Taking advantage of genetic engineering and live-cell microscopy, we performed time-lapse imaging of cells expressing fluorescently tagged proteins under the control of their endogenous regulatory elements in order to follow their levels throughout the cell cycle. We effectively discern between cell cycle phases and S subphases based on fluorescence intensity and distribution of co-expressed proliferating cell nuclear antigen (PCNA)-mCherry. This allowed us to precisely determine and compare the levels and distribution of multiple replication-associated factors, including Rap1-interacting factor 1 (RIF1), minichromosome maintenance complex component 6 (MCM6), origin recognition complex subunit 1 (ORC1, and Claspin, with high spatiotemporal resolution in HeLa Kyoto cells. Combining these data with available mass spectrometry-based measurements of protein concentrations reveals the changes in the concentration of these proteins throughout the cell cycle. Our approach provides a practical basis for a detailed interrogation of protein dynamics in the context of the cell cycle. Full article

Canopy volume is a crucial biological parameter for assessing tree growth, accurately estimating forest Above-Ground Biomass (AGB), and evaluating ecosystem stability. Airborne Laser Scanning (ALS) and Terrestrial Laser Scanning (TLS) are advanced precision mapping technologies that capture highly accurate point clouds for forest digitization studies. Despite advances in calculating canopy volume, challenges remain in accurately extracting the canopy and removing gaps. This study proposes a canopy volume extraction method based on an improved PointNeXt model, fusing ALS and TLS point cloud data. In this work, improved PointNeXt is first utilized to extract the canopy, enhancing extraction accuracy and mitigating under-segmentation and over-segmentation issues. To effectively calculate canopy volume, the canopy is divided into multiple levels, each projected into the xOy plane. Then, an improved Mean Shift algorithm, combined with KdTree, is employed to remove gaps and obtain parts of the real canopy. Subsequently, a convex hull algorithm is utilized to calculate the area of each part, and the sum of the areas of all parts multiplied by their heights yields the canopy volume. The proposed method’s performance is tested on a dataset comprising poplar, willow, and cherry trees. As a result, the improved PointNeXt model achieves a mean intersection over union (mIoU) of 98.19% on the test set, outperforming the original PointNeXt by 1%. Regarding canopy volume, the algorithm’s Root Mean Square Error (RMSE) is 0.18 m³, and a high correlation is observed between predicted canopy volumes, with an R-Square (R²) value of 0.92. Therefore, the proposed method effectively and efficiently acquires canopy volume, providing a stable and accurate technical reference for forest biomass statistics. Full article

The potential for grapes and wine to be tainted following vineyard exposure to wildfire smoke is well established, with recent studies suggesting hops and apples (and thus beer and cider) can be similarly affected. However, the susceptibility of other crops to ‘smoke taint’ has not yet been investigated. Smoke was applied to a selection of fruits and vegetables, as well as potted lavender plants, and their volatile phenol composition determined by gas chromatography–mass spectrometry to evaluate their susceptibility to contamination by smoke. Volatile phenols were observed in control (unsmoked) capsicum, cherry, lavender, lemon, spinach and tomato samples, typically at ≤18 µg/kg, but 52 µg/kg of guaiacol and 83–416 µg/kg of o- and m-cresol and 4-methylsyringol were detected in tomato and lavender samples, respectively. However, significant increases in volatile phenol concentrations were observed as a consequence of smoke exposure; with the highest volatile phenol levels occurring in smoke-exposed strawberry and lavender samples. Variation in the uptake of volatile phenols by different crops was attributed to differences in their physical properties, i.e., their surface area, texture and/or cuticle composition, while the peel of banana, lemon, and to a lesser extent apple samples, mitigated the permeation of smoke-derived volatile phenols into pulp. Results provide valuable insight into the susceptibility of different crops to smoke contamination. Full article

Fluorescence resonance energy transfer (FRET) biosensors have proven to be an indispensable tool in cell biology and, more specifically, in the study of G-protein signalling. The best method of measuring the activation status or FRET state of a biosensor is often fluorescence lifetime imaging microscopy (FLIM), as it does away with many disadvantages inherent to fluorescence intensity-based methods and is easily quantitated. Despite the significant potential, there is a lack of reliable FLIM-FRET biosensors, and the data processing and analysis workflows reported previously face reproducibility challenges. Here, we established a system in live primary mouse pancreatic ductal adenocarcinoma cells, where we can detect the activation of an mNeonGreen-Gαi3-mCherry-Gγ2 biosensor through the lysophosphatidic acid receptor (LPAR) with 2-photon time-correlated single-photon counting (TCSPC) FLIM. This combination gave a superior signal to the commonly used mTurquoise2-mVenus G-protein biosensor. This system has potential as a platform for drug screening, or to answer basic cell biology questions in the field of G-protein signalling. Full article

A recombinant Ross River virus (RRV) that contains the fluorescent protein mCherry fused to the non-structural protein 3 (nsP3) was constructed, which allowed real-time imaging of viral replication. RRV-mCherry contained either the natural opal stop codon after the nsP3 gene or was constructed without a stop codon. The mCherry fusion protein did not interfere with the viral life cycle and deletion of the stop codon did not change the replication capacity of RRV-mCherry. Comparison of RRV-mCherry and chikungunya virus-mCherry infections, however, showed a cell type-dependent delay in RRV-mCherry replication in HEK 293T cells. This delay was not caused by differences in cell entry, but rather by an impeded nsP expression caused by the RRV inhibitor ZAP (zinc finger CCCH-Type, antiviral 1). The data indicate that viral replication of alphaviruses is cell-type dependent, and might be unique for each alphavirus. Full article

Accurately identifying cherry-tomato picking points and obtaining their coordinate locations is critical to the success of cherry-tomato picking robots. However, previous methods for semantic segmentation alone or combining object detection with traditional image processing have struggled to accurately determine the cherry-tomato picking point due to challenges such as leaves as well as targets that are too small. In this study, we propose a YOLOv8n-DDA-SAM model that adds a semantic segmentation branch to target detection to achieve the desired detection and compute the picking point. To be specific, YOLOv8n is used as the initial model, and a dynamic snake convolutional layer (DySnakeConv) that is more suitable for the detection of the stems of cherry-tomato is used in neck of the model. In addition, the dynamic large convolutional kernel attention mechanism adopted in backbone and the use of ADown convolution resulted in a better fusion of the stem features with the neck features and a certain decrease in the number of model parameters without loss of accuracy. Combined with semantic branch SAM, the mask of picking points is effectively obtained and then the accurate picking point is obtained by simple shape-centering calculation. As suggested by the experimental results, the proposed YOLOv8n-DDA-SAM model is significantly improved from previous models not only in detecting stems but also in obtaining stem’s masks. In the [email protected] and F1-score, the YOLOv8n-DDA-SAM achieved 85.90% and 86.13% respectively. Compared with the original YOLOv8n, YOLOv7, RT-DETR-l and YOLOv9c, the [email protected] has improved by 24.7%, 21.85%, 19.76%, 15.99% respectively. F1-score has increased by 16.34%, 12.11%, 10.09%, 8.07% respectively, and the number of parameters is only 6.37M. In the semantic segmentation branch, not only does it not need to produce relevant datasets, but also improved its mIOU by 11.43%, 6.94%, 5.53%, 4.22% and [email protected] by 12.33%, 7.49%, 6.4%, 5.99% compared to Deeplabv3+, Mask2former, DDRNet and SAN respectively. In summary, the model can well satisfy the requirements of high-precision detection and provides a strategy for the detection system of the cherry-tomato. Full article

The success of establishing fruit orchards has traditionally been attributed to the vigor of the nursery plant used. This study aimed to evaluate the post-transplant survival, canopy growth and fruit productivity of two sweet cherry (Prunus avium L.) cultivars (‘Lapins’/‘Colt’ and ‘Regina’/‘Gisela 12’) with different radicular basal volumes of 100%, 50% and 25% and nursery plant types: (i) bare root (BR) or (ii) bagged (B). The initial stem diameter of the plants ranged from 12 to 19 mm, and their height ranged from 1.4 to 1.8 m. Plants grafted onto ‘Colt’ rootstock exhibited twice the initial root volume compared to those grafted onto ‘Gisela 12’. Evaluations were carried out in three commercial orchards during three seasons in the Central Valley of Chile. The results indicated that root volume and nursery type did not affect plant survival and productivity. For ‘Regina’/‘Gisela 12’, only the bag treatment resulted in less trunk cross-sectional area (TCSA) and shoot length, and for ‘Lapins’/‘Colt’, the BR25 treatment showed a lower initial TCSA than other treatments, although without a negative effect on yield. Hence, the presumption about the influence of root volume and plant type on the successful establishment of a sweet cherry on ‘Colt’ and ‘Gisela 12’ rootstock can be discarded. The survival, growth and precocity of the orchard depend more on post-planting conditions and water management than on the number or type of nursery plant roots. It is important to prioritize proper post-planting care and water management for optimal orchard health. Full article