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Datasets for "The Venturia inaequalis effector repertoire is expressed in waves, and is dominated by expanded families with predicted structural similarity to avirulence proteins "
<p>Datasets for preprint entitled "The <em>Venturia inaequalis</em> effector repertoire is expressed in waves, and is dominated by expanded families with predicted structural similarity to avirulence proteins from other fungi"</p> <p><strong>1) ViAnnotation.gff3</strong><br> Gene annotation of <em>Venturia inaequalis</em> MNH120 (<a href="https://genome.jgi.doe.gov/Venin1/Venin1.home.html">https://genome.jgi.doe.gov/Venin1/Venin1.home.html</a>) generated as part of the study "The <em>Venturia inaequalis</em> effector repertoire is expressed in waves, and is dominated by expanded families with predicted structural similarity to avirulence proteins from other fungi". </p> <p>Gene reannotation was performed to include genes that would have been missed in the previous annotation by Deng et al. (2017), especially those genes encoding putative effector proteins, which are difficult to predict. For this purpose, we used a three-step approach. In the first step, coding sequences (CDSs) from <em>V. inaequalis</em> isolate 05/172, which were predicted as part of a previous study by Passey et al. (2018) (<a href="https://journals.asm.org/doi/full/10.1128/MRA.01062-18">https://journals.asm.org/doi/full/10.1128/MRA.01062-18</a>), were downloaded from the National Center for Biotechnology Information (<a href="https://www.ncbi.nlm.nih.gov/nuccore/QFBF00000000.1/">https://www.ncbi.nlm.nih.gov/nuccore/QFBF00000000.1/</a>) and mapped to the MNH120 genome using GMAP v2021-02-22. In the second step, RNA-seq reads from one biological replicate representing each <em>in planta</em> time point of <em>Malus domestica</em> infection by <em>V. inaequalis </em>(12 hour post-inoculation [hpi], 24 hpi, 2 days post-inoculation [dpi], 3 dpi, 5 dpi, 7 dpi), as well as one time point representing growth of the fungus in culture, were mapped to the MNH120 genome using HISAT2 v2.2.1. Then, a genome-guided <em>de novo</em> transcriptome assembly was performed using Trinity v2.12.0 and likely CDSs were identified using Transdecoder v5.5.0 (<a href="https://github.com/TransDecoder/TransDecoder">https://github.com/TransDecoder/TransDecoder</a>) in conjunction with a minimum open frame (ORF) length of 50 amino acids. Finally, in the third step, all annotations were visualized in Geneious v9.05, together with the previous annotation from Deng et al. (2017), and a manual curation was performed to create a consensus prediction. Note: this reannotation was generated with the aim of identifying as many genes as possible, and as a result, it contains many spurious genes. </p> <p><strong>2) Protein_sequences_ViAnnotation.fasta</strong></p> <p><strong>3) ECs_Families_AlphaFold.zip</strong></p> <p>This dataset is made up of predicted protein tertiary structures representing the main member of each up-regulated <em>V. inaequalis</em> effector candidate family. Structures were predicted using Alphafold with the ColabFold server (<a href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb#scrollTo=rowN0bVYLe9n">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb#scrollTo=rowN0bVYLe9n</a>). In cases where the effector candidate had less than 30 proteins with amino acid sequence similarity in the NCBI database, a custom multiple sequence alignment (MSA) was generated and used as input for AlphaFold2. Here, mature protein sequences were used.</p> <p><strong>4) singletons_AlphaFold_OpenSourceCASP14.zip</strong></p> <p>This dataset set is made up of predicted protein tertiary structures representing up-regulated<em> V. inaequalis</em> singleton effector candidates. Structures were predicted using AlphaFold (<a href="https://github.com/deepmind/alphafold">https://github.com/deepmind/alphafold</a>) open source code v2.0.1 and v2.1.0, with pre-set casp14, max_template_date: 2020-05-14. Mature protein sequences were used as input. </p> <p><strong>5) ECs_Avrs_phytopathogens_AlphaFold.zip</strong></p> <p>Predicted tertiary structures of avirulence (Avr) proteins or candidate Avr proteins from other fungal pathogens included in the "The <em>Venturia inaequalis</em> effector repertoire is expressed in waves, and is dominated by expanded families with predicted structural similarity to avirulence proteins from other fungi" study. These structures were predicted using Alphafold with the ColabFold server (<a href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb#scrollTo=rowN0bVYLe9n">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb#scrollTo=rowN0bVYLe9n</a>). Mature protein sequences were used as input. </p> <p>If you have any questions about the datasets, please contact us.<br> Mercedes Rocafort: <a href="mailto:m.rocafort.ferrer@massey.ac.nz">m.rocafort.ferrer@massey.ac.nz</a><br> Carl Mesarich: <a href="mailto:c.mesarich@massey.ac.nz">c.mesarich@massey.ac.nz</a></p>
Genetic Modulation of Protein Expression in Rat Brain
<p><span>Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong <em>cis</em>-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared <em>cis</em>-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.</span><span> </span></p>
Light and confocal micrographs on the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, the accumulation of lipid droplets, and the heterologous expression and localisation of signature LD protein homologs to tobacco pollen tubes
<p>These micrographs accompany the work "Environmental gradients reveal stress hubs predating plant terrestrialization", posted as a pre-print on bioRxiv https://doi.org/10.1101/2022.10.17.512551 </p> <p>The light and confocal micrographs show the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, especially their accumulation of lipid droplets (LDs); in confocal micrographs, LDs appeared as distinct structures upon staining with BODIPY.</p> <p>Further confocal micrographs show the heterologous expression and localisation of signature LD protein homologs detected in Mesotaenium endlicherianum SAG 12.97; heterologous expression was carried out in tobacco pollen tubes were also stained with BODIPY and proteins were tagged with mCherry.</p>
Summary Statistics from "Genetically regulated gene expression and proteins revealed discordant effects" (LWAS of biomarker)
<p>Summary statistics of 92 blood protein levels. The corresponding publication is currently under revision.</p> <p> The zipped txt file is tab-delimited and contains the following columns:</p> <ul> <li>protein: protein name abbreviation</li> <li>cytoband: genomic region</li> <li>gene: gene name abbreviation</li> <li>setting: either "combined" (adj. for sex & age) or sex-stratified ("males", "females"; adj. for age)</li> <li>variant_id_hg19: SNP ID according to hg19</li> <li>variant_id_hg38: SNP ID according to hg19</li> <li>chr: chromosome</li> <li>pos_hg19: base position according to hg19</li> <li>pos_hg38: base position according to hg19</li> <li>effect_allele: also known as counted allele in additive model</li> <li>other_allele: not-counted allele</li> <li>eaf: effect allele frequency</li> <li>maf: minor allele frequency</li> <li>info: imputation info score</li> <li>n_samples: number of samples</li> <li>beta: effect estimate</li> <li>se: standard error</li> <li>zscore: Z-statistic</li> <li>pvalue: p-value</li> <li>FDR: FDR by gene and setting</li> <li>BBFDR: hierarchical FDR by setting</li> <li>hierFDR: TRUE if SNP is significant after hierarchical FDR</li> </ul>
Depletion of cap-binding protein eIF4E dysregulates amino acid metabolic gene expression
<p><span>Protein synthesis is </span><span>metabolically costly </span><span>and</span><span> must be tightly coordinated with </span><span>changing </span><span>cellular needs and nutrient availability. T</span><span>he cap-binding protein eIF4E</span><span> makes </span><span>the earliest contact between mRNAs and the translation machinery</span><span>, offering a key regulatory nexus</span><span>. </span><span>W</span><span>e acute</span><span>ly</span><span> deplet</span><span>ed</span> <span>this essential protein </span><span>and </span><span>found </span><span>s</span><span>urprisingly modest effects on cell growth and </span><span>recovery of </span><span>protein synthesis.</span><span> Paradoxically, </span><span>impaired protein biosynthesis upregulated </span><span>genes involved in catabolism of aromatic amino acids</span><span>simultaneously with the </span><span>induction of the </span><span>amino acid</span><span> biosynthetic regulon</span> <span>driven</span> <span>by </span><span>the integrated stress response factor</span> <span>GCN4</span><span>. </span><span>W</span><span>e</span><span> further</span><span> identified translation</span><span>al </span><span>control</span><span> of </span><span>PCL5</span><span>, </span><span>a negative regulator of Gcn4, that provides a consistent protein-to-mRNA ratio under varied translation environments. </span><span>This</span> <span>regulation </span><span>depende</span><span>d in part</span><span> on a uniquely long poly-(A) tract in the </span><span>PCL5</span><span> 5´ UTR and poly-(A) binding protein. Collectively, these results highlight</span> <span>how eIF4E connects</span> <span>protein synthesis </span><span>to</span> <span>metabolic gene regulation</span><span>,</span><span>uncover</span><span>ing</span><span> new mechanisms control</span><span>ling</span> <span>translation</span><span> during environmental challenges.</span></p>
Fig. 15 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 15. Trychosis breviterebratus sp. nov. (A-F, KPM-NK 75758) ― A, lateral habitus; B, dorsal habitus; C, frons, frontal view; D, head and mesosoma, lateral view; E, propodeum, dorsal view; F, right wings.
Fig. 14. Hylophasma luica Sheng, Li in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 14. Hylophasma luica Sheng, Li & Wang, 2019 (A-D, KPM-NK 75813; E, KPM-NK 75821) and Picardiella melanoleuca (Gravenhorst, 1829)(F-J, KPM-NK 75744) ― A, E, F, lateral habitus; B, G, dorsal habitus; C, H, head, frontal view; D, J, right fore wing; I, propodeum, dorsal view.
Fig. 13. Hoplocryptus sumiyona Uchida, 1956 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 13. Hoplocryptus sumiyona Uchida, 1956 (A-C, KPM-NK 76581) and H. toshimensis sp. nov. (E-I, KPM-NK 75797) ― A, E, dorsal habitus; B, F, head, frontal view; C, head and mesosoma, dorso-lateral view; D, lateral habitus; G, propodeum, dorsal view; H, right fore wing; I. metasoma, dorsal view.
Fig. 12 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 12. Hoplocryptus pini (Momoi, 1973) (A, D, F, KPM-NK 76578; B, E, KPM-NK 75780; C, G, KPM-NK 75774; H-J, 76580) ― A-C, H, lateral habitus; D, E, I, head, mesosoma and metasoma, dorsal view; F, J, head, frontal view; G, propodeum, dorsso-lateral view.
Fig. 10 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 10. Hoplocryptus ezoensis sp. nov. (A, C-F, KPM-NK 75799; B, KPM-NK 75802) and Ho. intermedius sp. nov. (G-K, KPM-NK 75806; L, M, KPM-NK 76582) ― A, G, L, lateral habitus; B, C, dorsal habitus; D, H, M, head, frontal view; E, J, propodeum, dorsal (E) and dorso-lateral (J) view; I, head and mesoscutum, dorso-lateral view; K, right fore wing.
Fig. 6. Caenocryptoides convergens Momoi, 1966 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 6. Caenocryptoides convergens Momoi, 1966 (A-C, TMNH) and Cryptus daidaigaster sp. nov. (D-J, NIAES) ― A, D, I, lateral habitus; B, E, head, mesosoma and metasoma, dorso-lateral view; C, F, J, head, frontal view; G, propodeum, dorsal view; H, right wings.
Fig. 2 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 2. Aritranis kuro sp. nov. (A, B, KPM-NK 75832); Buathra nipponica sp. nov. (C, D, KPM-NK 75746), Glabridorsum japonicum sp. nov. (E, KPM-NK 75742), Hoplocryptus ezoensis sp. nov. (F, KPM-NK 75799), Ho. intermedius sp. nov. (G, KPM-NK 75804), Ho. japonicus sp. nov. (H, KPM-NK 75771), Ho. maculatus sp. nov. (I, KPM-NK 75790, J, KPM-NK 75781, K, KPM-NK 75783), Hylophasma luica Sheng, Li & Wang, 2019 (L, M, KPM-NK 75813) and Trychosis breviterebratus sp. nov. (N, KPM-NK 75748), females ― A, F, G, H, M, propodeum and T I, dorsal (A, H, M) and lateral (F, G) view; B, E, L, T I, lateral view; C, I, propodeum, lateral (C) and dorsal (I) view; D, T I, lateral view; J, K, area basalis and part of anterior transverse carina of propodeum; N, metasoma, lateral view. Surface sculpture of right half of Fig. 2A omitted.
Fig. 1 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 1. Aritranis kuro sp. nov. (A, KPM-NK 75838); Buathra nipponica sp. nov. (B, C, KPM-NK 75746), Hoplocryptus ezoensis sp. nov. (D, KPM-NK 75799), Ho. ashoroensis sp. nov. (E, NIAES), Ho. intermedius sp. nov. (F, KPM-NK 75804), Ho. japonicus sp. nov. (G, KPM-NK 75771), Ho. maculatus sp. nov. (H, KPM-NK 75781), Ho. toshimensis sp. nov. (I, KPM-NK 75797), Hylophasma luica Sheng, Li & Wang, 2019 (J, K, KPM-NK 75813) and Trychosis breviterebratus sp. nov. (L-P, KPM-NK 75748), females ― A-D, J-M, head, frontal (A, B, D, J, L), lateral (C) and dorsal (K, M) view; E-I, apical margin of clypeus, frontal view; K, left mandible; O, left fore femur, anterior view; lower part of epicnemial carina, lateral view.
Fig. 5 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 5. Buathra nipponica sp. nov. (A-G, KPM-NK 75746; H, I, KPM-NK 75747) ― A, lateral habitus; B, mesosoma, lateral view; C, head, mesosoma and metasoma, dorsal view; D, frons, frontal view; E, propodeum, dorsal view; F, right fore wing; G, apex of metasoma, dorso-lateral view.
Fig. 9 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 9. Gotra elegans sp. nov. (A, C, D, KPM-NK 75822; B, E, KPM-NK 75823) and Hoplocryptus ashoroensis sp. nov. (F-J, NIAES) ― A, C, lateral habitus; B, dorsal habitus; C, H, head, frontal view; D, head, mesoscutum and scutellum, dorsal view; E, I, propodeum, dorsal view; J, right fore wing.
Fig. 4. Agrothereutes minousubae Nakanishi, 1965 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 4. Agrothereutes minousubae Nakanishi, 1965 (A, B, KPM-NK 76585; C, D, KPM-NK 76590) and Aritranis kuro sp. nov. (E, G, I, KPM-NK 75824; F, H, KPM-NK 75825; J, K, KPM-NK 76577) ― A, C, E, J, lateral habitus; B, tegula and humeral plate (red arrow), dorso-lateral view; D, G, K, head, frontal view; F, dorsal habitus; H, propodeum, dorsal view; I, right wings.
Fig. 7. Gambrus homonae Sonan, 1930 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 7. Gambrus homonae Sonan, 1930 (A, KPM-NK 76572; B-D, 76568; E, KPM-NK 76573) ― A, E, lateral habitus; B, head, frontal view; C, propodeum, dorsal view; D, right fore wing.
Fig. 3 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 3. Aritranis kuro sp. nov. (A, KPM-NK 75838), Buathra nipponica sp. nov. (B, KPM-NK 75746), Cryptus daidaigaster sp. nov. (C, NIAES), Gambrus homonae Sonan, 1930 (D, KPM-NK 76566); Glabridorsum japonicum sp. nov. (E, KPM-NK 75742), Gotra elegans sp. nov. (F, KPM-NK 75822); Hoplocryptus ashoroensis sp. nov. (G, NIAES), Ho. ezoensis sp. nov. (H, KPM-NK 75800), Ho. intermedius sp. nov. (I, KPM-NK 75804), Ho. japonicus sp. nov. (J, KPM-NK 75771), Ho. maculatus sp. nov. (K, KPM-NK 75781), Ho. pini (L, KPM-NK 76579), Ho. toshimensis sp. nov. (M, KPM-NK 75797), Picardiella melanoleuca (Gravenhorst, 1829) (N, KPM-NK 75744) and Trychosis breviterebratus sp. nov. (N, KPM-NK 75758), apex of ovipositor, lateral view.
Fig. 8 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 8. Glabridorsum japonicum sp. nov. (A, C, E, G, KPM-NK 75742; B, D, F, KPM-NK 75743) ― A, lateral habitus; B, head, mesosoma and metasoma, dorsal view; C, D, mesosoma, lateral view; E, head, frontal view; F, propodeum, dorsal view; G, apical part of right fore wing.
Fig. 5 in Expression profile of two HSP70 chaperone proteins in response to extreme thermal acclimation in Xestia c-nigrum (Lepidoptera: Noctuidae)
Fig. 5. Xc-HSC70 mRNA expression profiles induced by cold (−7 to 5 °C) and heat (37 to 47 °C) in 2nd, 3rd, 4th, 5th, and 6th instars and pupae of Xestia cnigrum. The relative quantities indicate the levels of the HSC70 gene transcript normalized against transcript levels of β-actin as an internal standard and compared with the transcript levels of the untreated control at 25 °C. An asterisk indicates a significant difference between the control and heat shock conditions (significant, * P <0.05). The data are denoted as the mean ± SEM (error bar).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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