Data_Sheet_1_A Growth-Promoting Bacteria, Paenibacillus yonginensis DCY84T Enhanced Salt Stress Tolerance by Activating Defense-Related Systems in Panax ginseng.docx

<p>Panax ginseng (C.A. Mayer) is a well-known medicinal plant used in traditional medicine in Korea that experiences serious salinity stress related to weather changes or incorrect fertilizer application. In ginseng, the use of Paenibacillus yonginensis DCY84^T to improve salt stress tolerance has not been thoroughly explored. Therefore, we studied the role of P. yonginensis DCY84^T under short-term and long-term salinity stress conditions in a controlled environment. In vitro testing of DCY84^T revealed high indole acetic acid (IAA) production, siderophore formation, phosphate solubilization and anti-bacterial activity. We determined that 10-min dip in 10¹⁰ CFU/ml DCY84^T was sufficient to protect ginseng against short-term salinity stress (osmotic stress) upon exposure to 300 mM NaCl treatment by enhancing nutrient availability, synthesizing hydrolyzing enzymes and inducing osmolyte production. Upon exposure to salinity stress (oxidative and ionic stress), strain DCY84^T-primed ginseng seedlings were protected by the induction of defense-related systems such as ion transport, ROS scavenging enzymes, proline content, total sugars, and ABA biosynthetic genes, as well as genes involved in root hair formation. Additionally, ginseng primed with DCY84^T and exposed to 300 mM NaCl showed the same metabolite profile as control ginseng plants, suggesting that DCY84^T effectively reduced salt stress. These results indicated that DCY84^T can be widely used as a microbial inoculant to protect ginseng plants against salinity stress conditions.</p

Data_Sheet_2_A Growth-Promoting Bacteria, Paenibacillus yonginensis DCY84T Enhanced Salt Stress Tolerance by Activating Defense-Related Systems in Panax ginseng.xlsx

<p>Panax ginseng (C.A. Mayer) is a well-known medicinal plant used in traditional medicine in Korea that experiences serious salinity stress related to weather changes or incorrect fertilizer application. In ginseng, the use of Paenibacillus yonginensis DCY84^T to improve salt stress tolerance has not been thoroughly explored. Therefore, we studied the role of P. yonginensis DCY84^T under short-term and long-term salinity stress conditions in a controlled environment. In vitro testing of DCY84^T revealed high indole acetic acid (IAA) production, siderophore formation, phosphate solubilization and anti-bacterial activity. We determined that 10-min dip in 10¹⁰ CFU/ml DCY84^T was sufficient to protect ginseng against short-term salinity stress (osmotic stress) upon exposure to 300 mM NaCl treatment by enhancing nutrient availability, synthesizing hydrolyzing enzymes and inducing osmolyte production. Upon exposure to salinity stress (oxidative and ionic stress), strain DCY84^T-primed ginseng seedlings were protected by the induction of defense-related systems such as ion transport, ROS scavenging enzymes, proline content, total sugars, and ABA biosynthetic genes, as well as genes involved in root hair formation. Additionally, ginseng primed with DCY84^T and exposed to 300 mM NaCl showed the same metabolite profile as control ginseng plants, suggesting that DCY84^T effectively reduced salt stress. These results indicated that DCY84^T can be widely used as a microbial inoculant to protect ginseng plants against salinity stress conditions.</p

A Multiprotein Complex Regulates Interference-Sensitive Crossover Formation in Rice

In most eukaryotes, a set of conserved proteins that are collectively termed ZMM proteins (named for molecular zipper 1 [ZIP1], ZIP2, ZIP3, and ZIP4, MutS homologue 4 [MSH4] and MSH5, meiotic recombination 3, and sporulation 16 [SPO16] in yeast [Saccharomyces cerevisiae]) are essential for the formation of the majority of meiotic crossovers (COs). Recent reports indicated that ZIP2 acts together with SPO16 and ZIP4 to control CO formation through recognizing and stabilizing early recombination intermediates in budding yeast. However, whether this mechanism is conserved in plants is not clear. Here, we characterized the functions of SHORTAGE OF CHIASMATA 1 (OsSHOC1; ZIP2 ortholog) and PARTING DANCERS (OsPTD; SPO16 ortholog) and their interactions with other ZMM proteins in rice (Oryza sativa). We demonstrated that disruption of OsSHOC1 caused a reduction of CO numbers to ∼83% of wild-type CO numbers, whereas synapsis and early meiotic recombination steps were not affected. Furthermore, OsSHOC1 interacts with OsPTD, which is responsible for the same set of CO formations as OsSHOC1. In addition, OsSHOC1 and OsPTD are required for the normal loading of other ZMM proteins, and conversely, the localizations of OsSHOC1 and OsPTD were also affected by the absence of OsZIP4 and human enhancer of invasion 10 in rice (OsHEI10). OsSHOC1 interacts with OsZIP4 and OsMSH5, and OsPTD interacts with OsHEI10. Furthermore, bimolecular fluorescence complementation and yeast-three hybrid assays demonstrated that OsSHOC1, OsPTD, OsHEI10, and OsZIP4 were able to form various combinations of heterotrimers. Moreover, statistical and genetic analysis indicated that OsSHOC1 and OsPTD are epistatic to OsHEI10 and OsZIP4 in meiotic CO formation. Taken together, we propose that OsSHOC1, OsPTD, OsHEI10, and OsZIP4 form multiple protein complexes that have conserved functions in promoting class I CO formation

Additional file 2 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 2. Table S2. PFS association statistics for clinical variables and molecular features e.g. p-value, HR ratio, median PFS

Additional file 5 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 5. Table S5. Summary of oncogenic events in paired PDtumors. Endocrine therapy: endocrine therapy in combination with Palbo treatment

Additional file 1 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 1. Table S1. Sample-levelannotation including patient clinical attributes, tumor characteristics andgenomic/molecular features

Additional file 3 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 3. Table S3. PFS associationstatistics for gene signatures (GSVA scores)

Additional file 6 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 6. Fig. S1. Kaplan-Meier plots of poor prognostic biomarkers. Fig. S2. Characteristics of the HRD-high cluster. Fig. S3. Characteristics of HRD-high tumors co-occurring with TP53 mutation. Fig. S4. Kaplan-Meier plots of expression-based prognosis markers. Fig. S5. Proliferative cluster enriched in poor prognostic markers. Fig. S6. Integrative analysis identified distinct prognostic clusters. Fig. S7. Molecular characteristics of integrative clusters. Fig. S8. Subtype switching driven by changes in PAM50 score composition. Fig. S9. Increased tumor growth and proliferation at PD. Fig. S10. IHC analysis of cell cycle markers. Fig. S11. Landscape of PD-specific genomic alterations. Fig. S12. RB1 LOF associated with increased APOBEC signature at PD. Fig. S13. APOBEC signature enriched in PD-specific tumor subclones

Additional file 4 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 4. Table S4. Comparison of genomic alteration prevalence at BL vs. PD