Table2_In-depth analysis of large-scale screening of WRKY members based on genome-wide identification.XLSX

With the rapid advancement of high-throughput sequencing technology, it is now possible to identify individual gene families from genomes on a large scale in order to study their functions. WRKY transcription factors are a key class of regulators that regulate plant growth and abiotic stresses. Here, a total of 74 WRKY genes were identified from Dendrobium officinale Kimura et Migo genome. Based on the genome-wide analysis, an in-depth analysis of gene structure and conserved motif was performed. The phylogenetic analysis indicated that DoWRKYs could be classified into three main groups: I, II, and III, with group II divided into five subgroups: II-a, II-b, II-c, II-d, and II-e. The sequence alignment indicated that these WRKY transcriptional factors contained a highly conserved WRKYGQK heptapeptide. The localization analysis of chromosomes showed that WRKY genes were irregularly distributed across several chromosomes of D. officinale. These genes comprised diverse patterns in both number and species, and there were certain distinguishing motifs among subfamilies. Moreover, the phylogenetic tree and chromosomal location results indicated that DoWRKYs may have undergone a widespread genome duplication event. Based on an evaluation of expression profiles, we proposed that DoWRKY5, 54, 57, 21, etc. may be involved in the transcriptional regulation of the JA signaling pathway. These results provide a scientific reference for the study of DoWRKY family genes.</p

Table1_In-depth analysis of large-scale screening of WRKY members based on genome-wide identification.XLSX

With the rapid advancement of high-throughput sequencing technology, it is now possible to identify individual gene families from genomes on a large scale in order to study their functions. WRKY transcription factors are a key class of regulators that regulate plant growth and abiotic stresses. Here, a total of 74 WRKY genes were identified from Dendrobium officinale Kimura et Migo genome. Based on the genome-wide analysis, an in-depth analysis of gene structure and conserved motif was performed. The phylogenetic analysis indicated that DoWRKYs could be classified into three main groups: I, II, and III, with group II divided into five subgroups: II-a, II-b, II-c, II-d, and II-e. The sequence alignment indicated that these WRKY transcriptional factors contained a highly conserved WRKYGQK heptapeptide. The localization analysis of chromosomes showed that WRKY genes were irregularly distributed across several chromosomes of D. officinale. These genes comprised diverse patterns in both number and species, and there were certain distinguishing motifs among subfamilies. Moreover, the phylogenetic tree and chromosomal location results indicated that DoWRKYs may have undergone a widespread genome duplication event. Based on an evaluation of expression profiles, we proposed that DoWRKY5, 54, 57, 21, etc. may be involved in the transcriptional regulation of the JA signaling pathway. These results provide a scientific reference for the study of DoWRKY family genes.</p

Additional file 1 of Genome sequencing-based transcriptomic analysis reveals novel genes in Peucedanum praeruptorum

Additional file 1:Figure S1. Expression profile analysis of ATG family genes before and after bolting. Table S1. KO-enriched terms and genes in the two groups of samples before and after bolting. Table S2. GO functional classification terms and genes of two groups of samples before and after bolting. Table S3. Differentially expressed transcription factors in two samples before and after bolting. Table S4. Source and target genes for differential protein interaction network construction. Table S5. FPKM values and annotation information of five gene families in two samples before and after bolting

Image_1_Label-Free Quantitative Proteomics Unravel the Impacts of Salt Stress on Dendrobium huoshanense.JPEG

Salt stress is a constraint on crop growth and productivity. When exposed to high salt stress, metabolic abnormalities that disrupt reactive oxygen species (ROS) homeostasis result in massive oxygen radical deposition. Dendrobium huoshanense is a perennial orchid herb that thrives in semi-shade conditions. Although lots of studies have been undertaken on abiotic stresses (high temperature, chilling, drought, etc.) of model plants, few studies were reported on the mechanism of salt stress in D. huoshanense. Using a label-free protein quantification method, a total of 2,002 differential expressed proteins were identified in D. huoshanense. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that proteins involved in vitamin B6 metabolism, photosynthesis, spliceosome, arginine biosynthesis, oxidative phosphorylation, and MAPK signaling were considerably enriched. Remarkably, six malate dehydrogenases (MDHs) were identified from deferentially expressed proteins. (NAD+)-dependent MDH may directly participate in the biosynthesis of malate in the nocturnal crassulacean acid metabolism (CAM) pathway. Additionally, peroxidases such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as antioxidant enzymes involved in glutathione biosynthesis and some vitamins biosynthesis were also identified. Taken together, these results provide a solid foundation for the investigation of the mechanism of salt stress in Dendrobium spp.</p

Table_1_Label-Free Quantitative Proteomics Unravel the Impacts of Salt Stress on Dendrobium huoshanense.XLS

Salt stress is a constraint on crop growth and productivity. When exposed to high salt stress, metabolic abnormalities that disrupt reactive oxygen species (ROS) homeostasis result in massive oxygen radical deposition. Dendrobium huoshanense is a perennial orchid herb that thrives in semi-shade conditions. Although lots of studies have been undertaken on abiotic stresses (high temperature, chilling, drought, etc.) of model plants, few studies were reported on the mechanism of salt stress in D. huoshanense. Using a label-free protein quantification method, a total of 2,002 differential expressed proteins were identified in D. huoshanense. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that proteins involved in vitamin B6 metabolism, photosynthesis, spliceosome, arginine biosynthesis, oxidative phosphorylation, and MAPK signaling were considerably enriched. Remarkably, six malate dehydrogenases (MDHs) were identified from deferentially expressed proteins. (NAD+)-dependent MDH may directly participate in the biosynthesis of malate in the nocturnal crassulacean acid metabolism (CAM) pathway. Additionally, peroxidases such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as antioxidant enzymes involved in glutathione biosynthesis and some vitamins biosynthesis were also identified. Taken together, these results provide a solid foundation for the investigation of the mechanism of salt stress in Dendrobium spp.</p

Table_2_Label-Free Quantitative Proteomics Unravel the Impacts of Salt Stress on Dendrobium huoshanense.XLSX

Salt stress is a constraint on crop growth and productivity. When exposed to high salt stress, metabolic abnormalities that disrupt reactive oxygen species (ROS) homeostasis result in massive oxygen radical deposition. Dendrobium huoshanense is a perennial orchid herb that thrives in semi-shade conditions. Although lots of studies have been undertaken on abiotic stresses (high temperature, chilling, drought, etc.) of model plants, few studies were reported on the mechanism of salt stress in D. huoshanense. Using a label-free protein quantification method, a total of 2,002 differential expressed proteins were identified in D. huoshanense. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that proteins involved in vitamin B6 metabolism, photosynthesis, spliceosome, arginine biosynthesis, oxidative phosphorylation, and MAPK signaling were considerably enriched. Remarkably, six malate dehydrogenases (MDHs) were identified from deferentially expressed proteins. (NAD+)-dependent MDH may directly participate in the biosynthesis of malate in the nocturnal crassulacean acid metabolism (CAM) pathway. Additionally, peroxidases such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as antioxidant enzymes involved in glutathione biosynthesis and some vitamins biosynthesis were also identified. Taken together, these results provide a solid foundation for the investigation of the mechanism of salt stress in Dendrobium spp.</p

Video S1.avi

A 2-second video of an optically trapped sperm without apparent rolling, with a frame rate of 200 fps and with 60× amplification in bright field. The contour of sperm head per frame was fitted with an ellipse

Video S2.avi

A representative 4-second video of a freely swimming sperm was shot with a frame rate of 40 fps and with 60× amplification in bright field

DataSheet_1_Deep learning radiomic analysis of DCE-MRI combined with clinical characteristics predicts pathological complete response to neoadjuvant chemotherapy in breast cancer.docx

ObjectiveThe aim of this study was to develop and validate a deep learning-based radiomic (DLR) model combined with clinical characteristics for predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in breast cancer. For early prediction of pCR, the DLR model was based on pre-treatment and early treatment dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data.Materials and methodsThis retrospective study included 95 women (mean age, 48.1 years; range, 29–77 years) who underwent DCE-MRI before (pre-treatment) and after two or three cycles of NAC (early treatment) from 2018 to 2021. The patients in this study were randomly divided into a training cohort (n=67) and a validation cohort (n=28) at a ratio of 7:3. Deep learning and handcrafted features were extracted from pre- and early treatment DCE-MRI contoured lesions. These features contribute to the construction of radiomic signature RS1 and RS2 representing information from different periods. Mutual information and least absolute shrinkage and selection operator regression were used for feature selection. A combined model was then developed based on the DCE-MRI features and clinical characteristics. The performance of the models was assessed using the area under the receiver operating characteristic curve (AUC) and compared using the DeLong test.ResultsThe overall pCR rate was 25.3% (24/95). One radiomic feature and three deep learning features in RS1, five radiomic features and 11 deep learning features in RS2, and five clinical characteristics remained in the feature selection. The performance of the DLR model combining pre- and early treatment information (AUC=0.900) was better than that of RS1 (AUC=0.644, P=0.068) and slightly higher that of RS2 (AUC=0.888, P=0.604) in the validation cohort. The combined model including pre- and early treatment information and clinical characteristics showed the best ability with an AUC of 0.925 in the validation cohort.ConclusionThe combined model integrating pre-treatment, early treatment DCE-MRI data, and clinical characteristics showed good performance in predicting pCR to NAC in patients with breast cancer. Early treatment DCE-MRI and clinical characteristics may play an important role in evaluating the outcomes of NAC by predicting pCR.</p

Video S3.avi

A 2-second video of the same sperm in Video S2, which was optically trapped and shot with a frame rate of 200 fps and with 60× amplification in bright field. The contour of sperm head per frame was fitted with an ellipse