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opennotspecifiedOct 2010View details →

FIGURE 5 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus

FIGURE 5. ML tree based on ITS2 sequences. Sequence data for the ITS2 was aligned from a total of 23 individuals from nine species. Demodex folliculorum and D. canis (GenBank nos. AM904564 and GU299785, respectively) were selected as the outgroups of ITS2 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).

opennotspecifiedMay 2021View details →

FIGURE 1 in Reinstatement of Alysicarpus pokleanus (Leguminosae, Papilionoideae: Desmodieae) based on ITS sequences of nuclear ribosomal DNA

FIGURE 1. Best ML tree obtained after analyzing 41 accessions from previous study (Gholami et al. 2017) including 3 outgroups using RaXML (Stamatakis 2014) on CIPRES Science gateway (Miller et al. 2010).

opencc-zeroMar 2023View details →

Supplementary material 1 from: Xu M, Liu Y, Möller E, LaGreca S, Moya P, Wang X, Timdal E, de Boer H, Barreno E, Wang L, Thüs H, Andrésson Ó, Magnússon KP, Ólafsdóttir ES, Heiðmarsson S (2023) Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland. MycoKeys 96: 57-75. https://doi.org/10.3897/mycokeys.96.100037

Multiple sequence alignment for fungal mtSSU primer design in the family Parmeliaceae (except for Usnea)

opencc-by-4.0Apr 2023View details →

Sequences of nuclear ribosomal internal transcribed spacer (ITS) for five Toxicodendron vernicifluum individuals

This dataset includes the aligned sequences of nuclear ribosomal internal transcribed spacer (ITS) for five Toxicodendron vernicifluum individuals sampled from China.

dryad32/100

The ribosome-inactivating proteins MAP30 and Momordin inhibit SARS-CoV-2

These data are related to a manuscript submitted to PLOS ONE. The recombinant proteins MAP30 and Momordin, prepared at the National Institute of Arthritis and Musculoskeletal and Skin Diseases, were analyzed for SARS-CoV-2 inhibition using A549-NLRV human lung cell assays performed at Southern Research during the Covid-19 pandemic. All viral inhibition and cell viability values reported can be derived from the raw data provided here. Some data are replicates. File dates correspond to those originally provided by and preserved at Southern Research, Birmingham AL.

opencc-zeroMay 2023View details →

opencc-by-4.0Jun 2023View details →

Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates

Python and Fiji code used for the study "Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates"

Fig. 4 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 4. - Circular gene tree of RIPs. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The phylogenetic tree was constructed using the maximum-likelihood method with the amino acid substitution model WAG + R9, ultrafast bootstrapping approximation (UFBoot) with 1000 iterations and the SH-like approximate likelihood ratio test with 1000 iterations. The legend titled 'Order (outer ring)' outlines the coloured dots around the perimeter of the tree and represents the phylogenetic order from which each protein sequence originated. Proteins without a coloured dot belong to orders with less than ten proteins. The legend titled 'RIP domains (inner lines)' defines colours in the branches of the tree, each representing a RIP group, based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 2. - The number and type of RIPs within each plant order. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 6. Tile plot of the most conserved amino acids within RIP domains of each protein group. The Y axis depicts the amino acid and corresponding position within the pokeweed antiviral protein (protein databank: 1QCI), the X axis depicts the proteins groups. For the two pink-highlighted amino acids on the Y axis, different amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. The solid blue cells represent amino acids conserved at least 70% within each RIP group and with shared identity to the reference sequence 1QCI. Patterned blue cells represent amino acids conserved at least 70% within RIP groups but without identity to 1QCI. Any amino acid positions with 70% consensus in less than three protein groups were collapsed and shaded black.

Fig. 3 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 3. - The number of RIPs within each plant species. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 1. - Physicochemical characteristics of different RIP groups. Values were calculated from the amino acid coding sequence of each protein in our dataset with the R package 'peptides' and presented on boxplot format. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (A) molecular weight prediction; (B) theoretical net charge prediction; (C) Boman potential protein interaction index prediction; (D) aliphatic index prediction.

Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. Colours indicate amino acids conserved in at least 70% of sequences. For the two pink-highlighted proteins, the black bolded amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. (A) Sequence alignment. RIP domain consensus: the consensus sequence generated from the multiple sequence alignment in Jalview excluding gaps; 1QCI: the amino acid sequence of pokeweed antiviral protein (protein databank: 1QCI). The third line denotes the similarity in the two sequences as determined by Clustal Omega. (B) The crystal structure of 1QCI visualized in UCSF ChimeraX in surface representation; (C) mesh representation; and (D) cartoon representation. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 3. Average biomass per surviving insect. Every day of the feeding experiment, the average weight per surviving insect was determined by weighing separate feeding cages with and without the surviving insects and dividing the difference in mass by the number of insects in that cage. This was done for the three repeats per treatment and the averages and standard errors are represented. Statistical differences on day 3 are represented by asterisks (*: p ≤ 0.05, **: p ≤ 0.01, ***: p ≤ 0.001).

Fig. 2 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 2. Effect of different concentrations of OsRIP1 compared on N. lugens survival and development. 30 insects (three cages with each 10 insects) were fed with artificial diet, supplemented with either different concentrations of OsRIP1 (0.75 μM, 1.5 μM or 3 μM), BSA (3 μM) or buffer only, for 3 days. Every day the artificial diet was refreshed, the surviving insects were counted and the developmental stage of each insect was assessed. Letters (a, b, c) denote statistical differences observed between treatments. (Jonckheere-Terpstra test with pairwise multiple comparisons, p <0.05).

Fig. 4 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 4. Effect of OsRIP1 on translation in a cell-free transcription/translation system based on insect cell extract. The dose dependent effect of recombinant OsRIP1 on the translation of luciferase was assessed using a luminometer. Percentage of translation (= percentage of luciferase activity) is shown as a function of OsRIP1 concentration. BSA was used as a control. Data of two independent replicates are shown.

Fig. 1. Transcript levels for OsRIP1 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 1. Transcript levels for OsRIP1 in rice shoots after high (A) or low (B) infestation with N. lugens. Expression of OsRIP1 in BPH infested seedlings was determined at different timepoints (3, 5, 6, 9 or 13 days post infestation (dpi)), relative to the transcript levels in mock treated plants. Bars represent mean expression values from three independent biological replicates (normalized to three reference genes), error bars indicate standard errors. Asterisks indicate statistically significant differences compared to expression levels in mock treated plants (*p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001).