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Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
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Fig. 1 in Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
Fig. 1. Sequence identification by matching a peptide fragmentation pattern to a predicted tryptic peptide sequence. (A) Example of the chicken weighted simple consensus (CWSC) sequence algorithm for predicting a tryptic collagen peptide sequence from a previously unsequenced taxon (ostrich) based on three related organisms with one weighted organism (chicken). If a consensus of at least two organisms was present at amino add residues that diverged (positions 11, 15, and 23), the consensus residue was chosen in the predicted tryptic peptide sequence. For residues that diverged where no consensus was present (positions 2 and 3), the residue from the weighted organism (chicken) was chosen for the predicted sequence. Amino acid residues that aligned through all three organisms were left unchanged in the predicted sequence. (B) The experimental MS/MS spectrum from the LC/MS/MS analysis of a triply charged peptide from ostrich bone protein extract that matched to the predicted sequence GPAGP (OH)PGKNGDDGEAGKP(OH)GRP(OH)GER and contained three hydroxyproline residues. (C) The MS/MS spectrum of the synthetically derived triply charged peptide of the same sequence for confirmation. The typical b- and y- fragment ions from the fragmentation pattern of the experimental peptide align very well with the synthetic peptide, validating the sequence interpretation
Fig. 2 in Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
Fig. 2. Collagen peptide sequences unique to extinct mastodon identified by LC/MS/MS. (A) The four collagen altl peptide sequences found by the approach that are unique to ancient mastodon. Xcorr (cross-correlation score) and Sp (preliminary score) represent the scores resulting from database searching against protein databases using Sequest. The asterisk represents the hydroxylation site after the posttranslationally modified residue. (B) An example of the experimental MS/MS spectrum of a doubly charged tryptic peptide for the collagen altl peptide sequence GSEGPQGTR from the LC/MS/MS analysis of mastodon fossilized bone extract identified from a Sequest search against a theoretical collagen protein database. (C) The synthetic version of the same peptide sequence. All major ions from the experimental spectrum align very well with the ions from the synthetic version, validating the sequence.
Fig. 2 in Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis.
Figure 1 in A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination
Figure 1. Tandem mass spectrum from high-resolution (HCD) fragmentation analysis of the peptide sequence (GPPGESGAVGPAGPIGSR) matched from our analysis of ostrich bone collagen that is homologous to the peptide proposed as unique to T. rex and B. canadensis.
Figure 2 in A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination
Figure 2. Tandem mass spectrum of the peptide sequence claimed as being endogenous to both dinosaurs with sequence (GLPGESGAVGPAGPPGSR) downloaded from the B. canadensis analysis by Schweitzer et al. [14].
Data from: A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo
Geographic distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g., recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, Heterosigma akashiwo. We compared the entire mitochondrial genome sequences of seven H. akashiwo strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates, were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of H. akashiwo.
Data from: The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera
Background: The eusocial Hymenoptera have radiated across a wide range of thermal environments, exposing them to significant physiological stressors. We reconstructed the evolutionary history of three families of Heat Shock Proteins (Hsp90, Hsp70, Hsp40), the primary molecular chaperones protecting against thermal damage, across 12 Hymenopteran species and four other insect orders. We also predicted and tested for thermal inducibility of eight Hsps from the presence of cis-regulatory heat shock elements (HSEs). We tested whether Hsp induction patterns in ants were associated with different thermal environments. Results: We found evidence for duplications, losses, and cis-regulatory changes in two of the three gene families. One member of the Hsp90 gene family, hsp83, duplicated basally in the Hymenoptera, with shifts in HSE motifs in the novel copy. Both copies were retained in bees, but ants retained only the novel HSE copy. For Hsp70, Hymenoptera lack the primary heat-inducible orthologue from Drosophila melanogaster and instead induce the cognate form, hsc70-4, which also underwent an early duplication. Episodic diversifying selection was detected along the branch predating the duplication of hsc70-4 and continued along one of the paralogue branches after duplication. Four out of eight Hsp genes were heat-inducible and matched the predictions based on presence of conserved HSEs. For the inducible homologues, the more thermally tolerant species, Pogonomyrmex barbatus, had greater Hsp basal expression and induction in response to heat stress than did the less thermally tolerant species, Aphaenogaster picea. Furthermore, there was no trade-off between basal expression and induction. Conclusions: Our results highlight the unique evolutionary history of Hsps in eusocial Hymenoptera, which has been shaped by gains, losses, and changes in cis-regulation. Ants, and most likely other Hymenoptera, utilize lineage-specific heat inducible Hsps, whose expression patterns are associated with adaptive variation in thermal tolerance between two ant species. Collectively, our analyses suggest that Hsp sequence and expression patterns may reflect the forces of selection acting on thermal tolerance in ants and other social Hymenoptera.
Integration of protein and coding sequences enables mutual augmentation of the language model
<p><strong>The file structure is as follows:</strong></p> <p>Project Root<br>├── TE_MRL<br>│ ├── MRL_dataset.zip<br>│ └── TE_dataset.zip<br>│<br>├── finetuned_model<br>│ ├── FoldP<br>│ ├── LocP<br>│ ├── SSP<br>│ └── SolP<br>│<br>├── tax_tsne<br>│ └── emb_3models.zip<br>│<br>└── training_data<br> ├── FoldP.csv<br> ├── LocP.csv<br> ├── SolP.csv<br> ├── SSP.pkl<br> └── pretrain_source_GCF.txt</p>
Sequence/simulation data for Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence
<p>This is a DOI-linked deposition of sequence/biophysical properties pairs used in the associated paper by Lotthammer et al:</p><p>Lotthammer, J. M.<strong>*</strong>, Ginell, G. M.<strong>*</strong>, Griffith, D.<strong>*</strong>, Emenecker, R. J. & Holehouse, A. S. <br>Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence.<br><i><strong>Nature Methods</strong></i> (<i>in press</i>), (2023).</p><p> </p>
A massive proteogenomic screen identifies thousands of novel human protein coding sequences
<p>Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. </p> <p>This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2022). </p>
Datasets for "Physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data"
<div> <p>Datasets used for implementing the <a href="https://github.com/huankoh/PSICHIC">PSICHIC</a> experiments shown in the <a href="https://doi.org/10.1101/2023.09.17.558145">manuscript</a>.</p> <p> </p> </div>
Convolutions are competitive with transformers for protein sequence pretraining
<p>- Pretrained models of protein sequences. See https://github.com/microsoft/protein-sequence-models for instructions on how to load models.</p> <p>- IDR datasets used for evaluation. </p> <p>- March 2020 version of UniRef50 with splits used for training. </p>
FASTA file of sequences of identified proteins in Anastrepha ludens reproductive tissues
<p>Seminal fluid proteins (Sfps) modify female phenotypes and have wide-ranging evolutionary implications on fitness in many insects. However, in the Mexican fruit fly, <em>Anastrepha ludens</em>, a highly destructive agricultural pest, the functions of Sfps are still largely unknown. To gain insights into female phenotypes regulated by Sfps, we used nano liquid chromatography mass spectrometry to conduct a proteomic analysis of the soluble proteins from reproductive organs of <em>A. ludens</em>. The proteins predicted to be transferred from males to females during copulation were 100 proteins from the accessory glands, 69 from the testes, and 20 from the ejaculatory bulb, resulting in 141 unique proteins after accounting for redundancies from multiple tissues. These 141 included orthologs to <em>Drosophila melanogaster</em> proteins involved mainly in oogenesis, spermatogenesis, immune response, lifespan, and fecundity. In particular, we found one protein associated with female olfactory response to repellent stimuli (Scribble), and two related to memory formation (aPKC, Shibire). Together, these results raise the possibility that <em>A. ludens</em> Sfps could play a role in regulating female olfactory responses and memory formation and could be indicative of novel evolutionary functions in this important agricultural pest.</p>
Highly significant improvement of protein sequence alignments with AlphaFold2
<p>Data, figures and tables from the manuscript "Highly significant improvement of protein sequence alignments with AlphaFold2" (https://doi.org/10.1093/bioinformatics/btac625).</p> <p>The repository containing all the steps to replicate the analysis is available at GitHub (https://github.com/cbcrg/msa-af2-nf).</p> <p>*The authors Athanasios Baltzis and Leila Mansouri contributed equally.</p>
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 (ECP1) sequences of five nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
Protein sequences for Dephosphorylation sites and fine-tuning notebook
<p>Protein sequences for Dephosphorylation sites</p>
Fig. 7 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 7 Immunolocalization of MSP in E. brevis sperm. a Immature spermatozoon from male. MSP is diffusely distributed in cytoplasm and concentrated in large granules (scale bar 10 µm). b Spermatozoon recovered from male and partially activated by 10-min incubation in sea water. MSP undergoes transformation resulting in appearance of
Fig. 5 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 5 Western blot analysis of MSP in E. brevis. a MSP has unusual mobility in gel and is found as protein with weight 36–38 kDa. Both male and female samples reveal MSP signal, because the latter include inseminated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Peptide competition assay confirms reactivity of anti-MSP antibodies with protein band of 36–38 kDa
Fig. 2 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 2 Western blot analysis of MSP in P. redivivus. In adult animals, MSP is detected as double band with approximate weight 15 and 16 kDa. a Both male and female samples reveal MSP signal, because the latter include mated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Analysis of young males and females. MSP is not detected in females, because most of them are unmated. Abbreviations: m, males; f, females
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Allen Brain Atlas
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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.
DANDI Archive for NWB datasets
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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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