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DNA and Cell Biology Apr 2021The fall armyworm () is one of the most significant agricultural pests in the world and invaded China in early 2019. We sampled and sequenced RNA-seq data from 15...
The fall armyworm () is one of the most significant agricultural pests in the world and invaded China in early 2019. We sampled and sequenced RNA-seq data from 15 individuals across different developmental stages. Developmental stages were the larval stage (5th instar larvae and 6th instar larvae), chrysalis stage, and adult stage (female adult and male adult). Individual samples were mainly clustered by developmental stages and we then identified variation between developmental stages of differentially expressed transcripts (DETs). There were 2136 upregulated DETs and 1391 downregulated DETs in the larval stage when comparing larval and chrysalis stages. In the comparison between the chrysalis and adult stages, there were 2033 upregulated DETs and 1391 downregulated DETs in the chrysalis stage. In total, 19,195 abundantly expressed transcripts were obtained and 10% of them were DETs. We then obtained stage-specific DETs to investigate the potential function of the fall armyworm during different developmental stages. We also constructed our annotation background set for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This indicated that the fall armyworm may undergo active metabolism during its lifespan, even in the chrysalis stage. And it also may experience detoxifying and xenobiotic metabolism throughout its life, especially in the larval stage, which partially explains the difficulty to eradicate using chemical control. Our study is the first insight into the developmental patterns of the fall armyworm and we also provide the fundamental information about enhanced drug resistance at the level of transcriptome. These results are beneficial for a future investigation related to the eradication and/or control stage.
Topics: Animals; China; Gene Expression; Gene Expression Regulation, Developmental; Gene Ontology; Larva; RNA-Seq; Spodoptera; Transcriptome
PubMed: 33761271
DOI: 10.1089/dna.2020.6191 -
Environmental Science and Pollution... Jan 2022We collected and processed Boletus edulis (King Bolete) carpophores grouped in four batches based on their developmental stage (button stage, young-white, large-white,...
We collected and processed Boletus edulis (King Bolete) carpophores grouped in four batches based on their developmental stage (button stage, young-white, large-white, and large-yellow). The study aimed, for the first time, to examine the B. edulis content and effect of braising and to estimate the intake of total mercury (THg) and methylmercury (MeHg) from a single meal based on whole (wet) weight (ww) and dry weight (dw). In braised carpophores, THg concentrations ranged from 0.2668 ± 0.0090 to 0.5434 ± 0.0071 mg kg ww at different developmental stages, whereas crude products concentrations ranged from 0.1880 ± 0.0247 to 0.2929 ± 0.0030 mg kg ww. The button stage crude carpophores were more highly contaminated with THg than at later stages of maturity, but MeHg levels were lower (p < 0.0001). On the other hand, braised button stage carpophores showed more MeHg than at later maturity stages. MeHg contributed at 1.9 ± 0.7% in THg in crude mushrooms and at 1.4 ± 0.3% in braised meals. The effect of braising was to increase the average THg and MeHg contents in fresh mushroom meals by 52 ± 31% and 53 ± 122% respectively, but a reduction of 40 ±14% and 40 ± 49% respectively was seen on a dw basis. The potential intakes of THg and MeHg from braised meals of B. edulis studied were small and considered safe.
Topics: Agaricales; Basidiomycota; Environmental Monitoring; Mercury; Methylmercury Compounds; Water Pollutants, Chemical
PubMed: 34386922
DOI: 10.1007/s11356-021-15884-1 -
Cell Reports Feb 2023During pre-implantation stages of mammalian development, maternally stored material promotes both the erasure of the sperm and oocyte epigenetic profiles and is...
During pre-implantation stages of mammalian development, maternally stored material promotes both the erasure of the sperm and oocyte epigenetic profiles and is responsible for concomitant genome activation. Here, we have utilized single-cell methylome and transcriptome sequencing (scM&T-seq) to quantify both mRNA expression and DNA methylation in oocytes and a developmental series of human embryos at single-cell resolution. We fully characterize embryonic genome activation and maternal transcript degradation and map key epigenetic reprogramming events in developmentally high-quality embryos. By comparing these signatures with early embryos that have undergone spontaneous cleavage-stage arrest, as determined by time-lapse imaging, we identify embryos that fail to appropriately activate their genomes or undergo epigenetic reprogramming. Our results indicate that a failure to successfully accomplish these essential milestones impedes the developmental potential of pre-implantation embryos and is likely to have important implications, similar to aneuploidy, for the success of assisted reproductive cycles.
Topics: Animals; Humans; Male; Multiomics; Semen; Embryonic Development; Embryo, Mammalian; Oocytes; Epigenesis, Genetic; Blastocyst; Mammals
PubMed: 36763500
DOI: 10.1016/j.celrep.2023.112100 -
American Journal of Botany Apr 2020The size and shape (physiognomy) of woody, dicotyledonous angiosperm leaves are correlated with climate. These relationships are the basis for multiple paleoclimate...
PREMISE
The size and shape (physiognomy) of woody, dicotyledonous angiosperm leaves are correlated with climate. These relationships are the basis for multiple paleoclimate proxies. Here we test whether Vitis exhibits phenotypic plasticity and whether physiognomy varies along the vine.
METHODS
We used Digital Leaf Physiognomy (DiLP) to measure leaf characters of four Vitis species from the USDA Germplasm Repository (Geneva, New York) from the 2012-2013 and 2014-2015 leaf-growing seasons, which had different environmental conditions.
RESULTS
Leaf shape changed allometrically through developmental stages; early stages were more linear than later stages. There were significant differences in physiognomy in the same developmental stage between the growing seasons, and species had significant differences in mean physiognomy between growing seasons. Phenotypic plasticity was defined as changes between growing seasons after controlling for developmental stage or after averaging all developmental stages. Vitis amurensis and V. riparia had the greatest phenotypic plasticity. North American species exhibited significant differences in tooth area:blade area. Intermediate developmental stages were most likely to exhibit phenotypic plasticity, and only V. amurensis exhibited phenotypic plasticity in later developmental stages.
CONCLUSIONS
Leaves have variable phenotypic plasticity along the vine. Environmental signal was strongest in intermediate developmental stages. This is significant for leaf physiognomic-paleoclimate proxies because these leaves are likely the most common in leaf litter and reflect leaves primarily included in paleoclimate reconstructions. Early season and early developmental stages have the potential to be confounding factors but are unlikely to exert significant influence because of differential preservation potential.
Topics: Climate; Environment; New York; Plant Leaves; Vitis
PubMed: 32270876
DOI: 10.1002/ajb2.1460 -
Journal of Experimental Botany Dec 2021Determining the grain yield potential contributed by grain number is a step towards advancing the yield of cereal crops. To achieve this aim, it is pivotal to recognize...
Determining the grain yield potential contributed by grain number is a step towards advancing the yield of cereal crops. To achieve this aim, it is pivotal to recognize the maximum yield potential (MYP) of the crop. In barley (Hordeum vulgare L.), the MYP is defined as the maximum spikelet primordia number of a spike. Many barley studies assumed the awn primordium (AP) stage to be the MYP stage regardless of genotypes and growth conditions. From our spikelet-tracking experiments using the two-rowed cultivar Bowman, we found that the MYP stage can be different from the AP stage. Importantly, we find that the occurrence of inflorescence meristem deformation and its loss of activity coincided with the MYP stage, indicating the end of further spikelet initiation. Thus, we recommend validating the barley MYP stage with the shape of the inflorescence meristem and propose this approach (named 'spikelet stop') for MYP staging. To clarify the relevance of AP and MYP stages, we compared the MYP stage and the MYP in 27 barley accessions (two- and six-rowed accessions) grown in the greenhouse and in the field. Our results reveal that the MYP stage can be reached at various developmental stages, which greatly depend on the genotype and growth conditions. Furthermore, we propose that the MYP stage and the time to reach the MYP stage can be used to determine yield potential in barley. Based on our findings, we suggest key steps for the identification of the MYP stage in barley that may also be applied in a related crop such as wheat.
Topics: Edible Grain; Hordeum; Inflorescence; Meristem; Triticum
PubMed: 34291795
DOI: 10.1093/jxb/erab342 -
Frontiers in Molecular Neuroscience 2022Noncoding RNAs (ncRNAs) occupy ~98% of the transcriptome in human, and are usually not translated into proteins. Among ncRNAs, long non-coding RNAs (lncRNAs, >200...
Noncoding RNAs (ncRNAs) occupy ~98% of the transcriptome in human, and are usually not translated into proteins. Among ncRNAs, long non-coding RNAs (lncRNAs, >200 nucleotides) are important regulators to modulate gene expression, and are involved in many biological processes (e.g., cell development). To study lncRNA regulation, many computational approaches or tools have been proposed by using bulk transcriptomics data. Nevertheless, previous bulk data-driven methods are mostly limited to explore the lncRNA regulation regarding all of cells, instead of the lncRNA regulation specific to cell developmental stages. Fortunately, recent advance in single-cell sequencing data has provided a way to investigate cell developmental stage-specific lncRNA regulation. In this work, we present a novel computational method, CDSlncR (Cell Developmental Stage-specific lncRNA regulation), which combines putative lncRNA-target binding information with single-cell transcriptomics data to infer cell developmental stage-specific lncRNA regulation. For each cell developmental stage, CDSlncR constructs a cell developmental stage-specific lncRNA regulatory network in the cell developmental stage. To illustrate the effectiveness of CDSlncR, we apply CDSlncR into single-cell transcriptomics data of the developing human neocortex for exploring lncRNA regulation across different human neocortex developmental stages. Network analysis shows that the lncRNA regulation is unique in each developmental stage of human neocortex. As a case study, we also perform particular analysis on the cell developmental stage-specific lncRNA regulation related to 18 known lncRNA biomarkers in autism spectrum disorder. Finally, the comparison result indicates that CDSlncR is an effective method for predicting cell developmental stage-specific lncRNA targets. CDSlncR is available at https://github.com/linxi159/CDSlncR.
PubMed: 36710930
DOI: 10.3389/fnmol.2022.1037565 -
Journal of Fungi (Basel, Switzerland) Jul 2021The dichloromethane extraction was applied to extracted volatile compounds of the six developmental stages of caps and stipes of an mushroom and the relative contents...
The dichloromethane extraction was applied to extracted volatile compounds of the six developmental stages of caps and stipes of an mushroom and the relative contents were measured with the gas chromatography-mass spectrometry. The number of identified compounds ranged between 53 and 52, respectively, with a high ratio of alkane volatiles. The significant differences between the aroma compounds were determined in caps to identify their stages of development. The fully mature stage caps were characterized by 4,6-dimethyl-dodecane (7.69 ± 1.15%), 2-hexyl-1-decanol (11.8 ± 1.61%), 1,3-di-tert-butylbenzene (11.4 ± 1.25%), heptadecyl pentadecafluorooctanoate (2.16 ± 0.31%), and 2-hexyl-1-dodecanol (13.5 ± 1.33%). Niacinamide (3.90 ± 0.07%) and glycerol (3.62 ± 1.27%) was present in the caps in the early-stage of the rotting mushroom, which represented the 10th-12th day of fructification. The caps and stipes from the 12th-15th day of fructification were characterized by 2,3-butanediol (11.7 ± 0.13% and 8.00 ± 0.10%, respectively). Moreover, the caps from this developmental stage were characterized by 2-methyl- and 3-methyl butanoic acids (0.18 ± 0.03% and 0.33 ± 0.02%, respectively) which are typical for the rotting stage. In this study, we confirmed the effect of developmental stages on the aroma profile.
PubMed: 34436150
DOI: 10.3390/jof7080611 -
Journal of Orofacial Orthopedics =... May 2021The aim of this study was to comparatively evaluate hand-wrist bones, cervical vertebrae and tooth development stages according to skeletal classification.
PURPOSE
The aim of this study was to comparatively evaluate hand-wrist bones, cervical vertebrae and tooth development stages according to skeletal classification.
METHODS
The orthodontic initial records of 297 patients were used and separated into three groups according to the skeletal malocclusion. Three groups including 99 people each were sampled representing malocclusions with Angle classes I, II and III, respectively. The panoramic, cephalometric and hand-wrist radiographs of all patients included in this study were used to compare dental and skeletal maturation indicators. Calcification of teeth was rated according to the system of Demirjian. To evaluate the stage of skeletal maturation hand-wrist radiographs were analyzed according to the Grave and Brown method. Also, Hassel and the Farman method was used to classifying vertebral developmental stages. Spearman rank correlation tests, as well as Fisher exact χ tests with r×c tables, were used for the comparison of categorical variables.
RESULTS
Hand-wrist, vertebral and dental development stages showed a statistically significant relationship (p < 0.01) for both genders and in all malocclusions. The association between the different maturation indicators used in this study and the type of malocclusion was also statistically significant for both genders. It was observed that the peak period of skeletal maturation according to the hand-wrist radiograph findings correlated with the cervical vertebrae stage C3 in girls (63.2%) and C2-C3 in boys (43.5-43.5%). The weakest correlation was seen between the dental development stages and the skeletal developmental stages in the class II group (r = 0.443-0.220 [girls]; r = 0.604-0.410 [boys]).
CONCLUSION
The use of the dental development stage as a reliable indicator of maturation was limited. According to the Demirjian method, the calcification stage of the second molar might indicate that the individual is in the pubertal peak period.
Topics: Age Determination by Skeleton; Calcification, Physiologic; Cephalometry; Cervical Vertebrae; Female; Humans; Male; Malocclusion; Tooth; Wrist
PubMed: 33725143
DOI: 10.1007/s00056-021-00286-2 -
Developmental Dynamics : An Official... Oct 2023Lesser sandeel (Ammodytes marinus) is widely distributed in North Sea ecosystems. Sandeel acts as a critical trophic link between zooplankton and top predators (fish,...
BACKGROUND
Lesser sandeel (Ammodytes marinus) is widely distributed in North Sea ecosystems. Sandeel acts as a critical trophic link between zooplankton and top predators (fish, mammals, sea birds). Because they live buried in the sand, sandeel may be directly affected by the rapid expansion of anthropogenic activities linked to their habitat on the sea bottom (e.g., hydrocarbon extraction, offshore renewable energy, and subsea mining). It is, therefore, important to understand the impact of cumulative environmental and anthropogenic stressors on this species. A detailed description of the ontogenetic timeline and developmental staging for this species is lacking limiting the possibilities for comparative developmental studies assessing, e.g., the impact of various environmental stressors.
RESULTS
A detailed description of the morphological development of lesser sandeel and their developmental trajectory, obtained through visual observations and microscopic techniques, is presented. Methods for gamete stripping and intensive culture of the early life stages are also provided.
CONCLUSION
This work provides a basis for future research to understand the effect of cumulative environmental and anthropogenic stressors on development in the early life stages of lesser sandeel.
Topics: Animals; Ecosystem; Perciformes; Fishes; Birds; Germ Cells; Mammals
PubMed: 37306183
DOI: 10.1002/dvdy.634 -
Frontiers in Plant Science 2022Benzothiadiazole (BTH) is a functional analogue of salicylic acid able to induce systemic acquired resistance in many horticultural crops. The aim of the work was to...
Benzothiadiazole (BTH) is a functional analogue of salicylic acid able to induce systemic acquired resistance in many horticultural crops. The aim of the work was to investigate how BTH may affect i) fruit quality, ii) ascorbic acid (AsA) oxidation and recycling metabolism and iii) phenolic compounds accumulation, during development and ripening of berries from the two selected cultivars. Blueberry ( L.) plants (cv 'Brigitta' and 'Duke') were treated with 0.118 mM BTH every two weeks during ripening, then all fruits of each plant were harvested and divided in four developmental stages. Results indicated that BTH had no marked effects on fruit quality parameters. During the first developmental stage, BTH negatively affected dry matter in both cv, while soluble solids and AsA content were affected in 'Duke'. In fully ripe berries, BTH reduced dry matter in 'Duke' and enhanced soluble solids content in 'Brigitta', while diminishing titratable acidity. AsA content was positively affected by BTH in 'Duke', but not in 'Brigitta'. The effect of BTH on the enzymes involved in AsA recycling was recorded in berries at the third (fruit more than half pigmented) and fourth developmental stages. After treatment, in both cv ascorbate peroxidase (APX) activity increased in fully ripe berries, while monodehydroascorbate reductase (MDHAR) activity was stimulated at the third ripening stage. Conversely, the activities of dehydroascorbate reductase (DHAR) and glutathione reductase (GR) were enhanced only in 'Brigitta' and in 'Duke', respectively. BTH stimulated total polyphenols, flavonoid and anthocyanin accumulation in 'Brigitta' and in 'Duke' at the third and fourth ripening stages. In fully ripe berries, BTH enhanced the accumulation of delphinidins, cyanidins, petunidins and peonidins in 'Brigitta', while in 'Duke' it increased all classes of anthocyanidins, including malvidin. On the contrary, the relative proportion of the individual anthocyanins was only slightly affected by BTH treatment, mainly regarding delphinidin and malvidin at the third and fourth stage of ripening of 'Duke' and 'Brigitta', respectively. These results show that preharvest BTH application can positively impact on fruit bioactive compounds levels, affecting AsA recycling and content and increasing polyphenols accumulation in fruit, but partly depending on cv and ripening stage.
PubMed: 36570922
DOI: 10.3389/fpls.2022.1032133