Additional data for the paper Gyaltshen, Rozenberg et al (2023) Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore Cymbomonas tetramitiformis, Genome Biology and Evolution.The files are as follows:Genome annotationInferno_Rfam.tblout - results of ncRNA predictiontRNA-ScanSE.tab - tRNA predictionsbraker_fixed.faa - protein sequencesbraker_fixed.gff - corrected gff gene annotationsbraker_original.gtf - original braker gene annotationseggnog.emapper.annotations - eggnog functional annotationsinterproscan.xml - interproscan functional annotations (xml)interproscan.tsv - interproscan functional annotations (tsv)RED.bed - genome masking (unmodified RED masking)masking.bed - genome masking (RED masking [subtracting regions of gene homologs in other prasinophytes] and viral elements)Viruses_mcl_genes.tsv - clustering and function predictions for genes from selected viral elements using remote homologyViruses_phylogeny_AG_03_multigene.jtree - multigene phylogeny of AG_03 and related viruses, in jtree formatViruses_phylogeny_PLVs_MCP.jtree - PLV phylogeny based on MCP, in jtree formatViruses_phylogeny_AG_03_multigene.jtreeViruses_phylogeny_AG_03_multigene.zipViruses_phylogeny_PLVs_MCP.jtreeViruses_phylogeny_PLVs_MCP.zipViruses_locations_including_fragments.bedViruses_representatives.zipjcf7180000139292_CtGEV.gbk - annotation of scaffold jcf7180000139292 (CtGEV with a PLVB insert) in Genbank formatjcf7180000174485_CHeCME.gbk - annotation of scaffold jcf7180000174485 (a CHeCME representative flanked by two near-identical RT genes) in Genbank formatBacteria.zip - bacterial scaffoldsBusco.zip - busco resultsCymbomonas_tetramitiformis_genome.gbf - annotated genome in Genbank formatCymbomonas_tetramitiformis_genome.faa - protein sequences in fasta format
Abstract While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells.
Anticancer agents induce a variety of adverse effects when administered to cancer patients. Busulfan is a known antileukemia agent. When administered for treatment of leukemia in young patients, busulfan could cause damage to the male reproductive system as one of its adverse effects, resulting in sterility.We investigated the effects of Korean Red Ginseng extract (KRGE) on busulfan-induced damage and/or dysfunction of the male reproductive system.We found that administration of busulfan to mice: decreased testis weight; caused testicular histological damage; reduced the total number of sperm, sperm motility, serum testosterone concentration; and eventually, litter size. Preadministration of KRGE partially attenuated various busulfan-induced damages to the male reproductive system. These results indicate that KRGE has a protective effect against busulfan-induced damage to the male reproduction system.The present study shows a possibility that KRGE could be applied as a useful agent to prevent or protect the male reproductive system from the adverse side effects induced by administration of anticancer agents such as busulfan.
Bulk and cell-specific CO2 fixation and PO4 uptake from Atlantic Explorer cruise AE1524 (BATS validation cruise BV50), September 2015.Phosphate uptake rates were measured in Prochlorococcus, Synechococcus, pigmented eukaryotes, and unpigmented eukaryotes.Also reported are CO2 fixation rate by Prochlorococcus, Synechococcus, and pigmented eukaryotes.
Formation of the cuticle from components of the secretory cavity and subcuticular wall was studied by transmission electron microscopy of glandular trichomes of Cannabis prepared by high pressure cryofixation-cryosubstitution. Secretory vesicles in the secretory cavity resembled those localized in the subcuticular wall as well as the vesicle-related material associated with the irregular inner surface of the cuticle and appeared to provide precursors for thickening of the cuticle. Some contiguous vesicles in the secretory cavity and subcuticular wall lacked a surface feature at their point of contact, supporting an interpretation of vesicle fusion. Fibrillar matrix from the secretory cavity contributed fibrillar matrix to the subcuticular wall, and persisted as residual fibrillar matrix associated with secretory materials coalesced to the thickened inner surface of the cuticle. Elongated fibrils arranged in uniformly spaced parallel pairs contributed to the organization of fibrillar matrix in the subcuticular wall. Striae were evident in the outer portion of the cuticle, and appeared to represent sites of degraded residual fibrillar matrix associated with secretory materials coalesced to the inner cuticular surface. This study supports an interpretation that contents of secretory vesicles from the secretory cavity contribute to formation of glandular cuticle.
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