Journal: PLoS ONE

Article Title: Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups

doi: 10.1371/journal.pone.0032867

Figure Lengend Snippet: After Walker et al. (2011). Groups labelled in black encompass the taxa listed in ; those in grey encompass the taxa in the EMBL/Genbank dbEST, and non-redundant protein and nucleotide databases. Blue = Opisthokonta, Brown = Amoebozoa, Magenta = Excavata, Green = Archaeplastida, Grey = CCTH Supergroup Red = SAR Supergroup, with stramenopile, alveolate and rhizarian labeled. Taxa in capitals contain multicellular species. Taxa highlighted contain species with nitrile hydratase genes. * = eukaryotic-type nitrile hydratase. Number of * indicates the number of subunits present. # = nitrile hydratase subunit genes that may be the result of prokaryotic contamination. Note that taxa branching from a single point represent nodes with ambiguous branching, and the eukaryotic tree is unrooted.

Article Snippet: BLASTp and tBLASTn searches of the Broad Institute Origins of Multicellularity website using the M. brevicollis nitrile hydratase protein sequence found similar sequences in the genomes of Salpingoeca rosetta , Thecamonas trahens and Sphaeroforma arctica (see ).

Techniques: Labeling

Journal: PLoS ONE

Article Title: Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups

doi: 10.1371/journal.pone.0032867

Figure Lengend Snippet: This form is known to be found in M. brevicollis, S. rosetta, S. diplocostata, S. arctica, T. trahens, A. anophagefferens, F. cylindrus, B. natans and E. huxleyi. The red area denotes the beta subunit, which is located N-terminally of the alpha subunit (green region). The CTLCSC active site is located in the alpha subunit, as shown by the shaded area. The yellow area denotes the histidine-rich stretch found between the subunit domains in opisthokonts.

Article Snippet: BLASTp and tBLASTn searches of the Broad Institute Origins of Multicellularity website using the M. brevicollis nitrile hydratase protein sequence found similar sequences in the genomes of Salpingoeca rosetta , Thecamonas trahens and Sphaeroforma arctica (see ).

Techniques:

Journal: Molecular Biology and Evolution

Article Title: Patterns of Ancestral Animal Codon Usage Bias Revealed through Holozoan Protists

doi: 10.1093/molbev/msy157

Figure Lengend Snippet: Whole Genome and Codon Usage Statistics in the Transcriptomes of the Three Holozoan Protists.

Article Snippet: Complete annotated transcriptome sequences for M. brevicollis and S. rosetta were downloaded from the Origins of Multicellularity Project at the Broad Institute; the C. owczarzaki transcriptome was downloaded from the EnsemblProtists database.

Techniques:

Journal: Molecular Biology and Evolution

Article Title: Patterns of Ancestral Animal Codon Usage Bias Revealed through Holozoan Protists

doi: 10.1093/molbev/msy157

Figure Lengend Snippet: Nc plots for M. brevicollis , S. rosetta and C. owczarzaki . GC3s values are shown on the x -axis and Nc values are given on the y -axis. The curved line on each plot represents the expected position of genes evolving under a neutral mutation model .

Article Snippet: Complete annotated transcriptome sequences for M. brevicollis and S. rosetta were downloaded from the Origins of Multicellularity Project at the Broad Institute; the C. owczarzaki transcriptome was downloaded from the EnsemblProtists database.

Techniques: Mutagenesis

Journal: Philosophical Transactions of the Royal Society B: Biological Sciences

Article Title: Choanoflagellates and the ancestry of neurosecretory vesicles

doi: 10.1098/rstb.2019.0759

Figure Lengend Snippet: Neurosecretory vesicle proteins in animals and their closest living relatives. (Top) Schematic model of the core molecular components of animal neurosecretory vesicles. (Below) Core proteins of animal neurosecretory vesicles can be assigned to ten categories: V-ATPases, vesicular neurotransmitter transporters, transporter and transporter-like proteins, proteins with four transmembrane domains, synapsins, synaptotagmins, secretory SNAREs, endosomal SNAREs, transiently associated proteins SNARE binding partners and co-chaperones (modified after ). Black dots indicate the presence of clear protein sequence homologues (also see electronic supplementary material, table S1), while lines indicate that a homologue was not detected in the respective organism. Taxonomic groupings are indicated as follows: brown box, Opisthokonta; red box, Holozoa; blue box, Metazoa; violet box, Bilateria; yellow box, Vertebrata. Phylogenetic tree based on a consensus phylogeny [ – ]. A. que , Amphimedon queenslandica ; B. den , Batrachochytrium dendrobatidis ; C. owc , Capsaspora owczarzaki ; D. rer , Danio rerio ; D. mel , Drosophila melanogaster ; H. sap , Homo sapiens ; M. bre , Monosiga brevicollis ; M. lei , Mnemiopsis leidyi ; N. vec , Nematostella vectensis ; R. ory , Rhizopus oryzae ; S. cer , Saccharomyces cerevisae ; S. pur , Strongylocentrotus purpuratus ; S. ros , Salpingoeca rosetta ; T. adh , Trichoplax adhaerens . B. den , R. ory and S. cer are fungi. * = protein of interest-like, a = putative SLC17A5-homologue, b = domain structure lost.

Article Snippet: Digital image stacks of the TEM sections of M. brevicollis and S. rosetta were imported into AMIRA (FEI Visualization Sciences Group) and aligned semi-manually.

Techniques: Binding Assay, Modification, Sequencing

Journal: Philosophical Transactions of the Royal Society B: Biological Sciences

Article Title: Choanoflagellates and the ancestry of neurosecretory vesicles

doi: 10.1098/rstb.2019.0759

Figure Lengend Snippet: Synaptobrevin in the choanoflagellate Salpingoeca rosetta . ( a ) Domain architecture of Salpingoeca rosetta synaptobrevin and Homo sapiens synaptobrevin 1 and 2. ( b ) Sequence alignment of the SNARE motif of S. rosetta synaptobrevin and H. sapiens synaptobrevin 1 and 2. The 15 layers (highlighted in blue including layers −1 to −7 and layers +1 to +8) important for SNARE complex formation are shown. The conserved arginine residues forming the ionic 0 layer are shown in green. ( c – c ″) Apical view of an S. rosetta cell stained with antibodies against ( c ) tubulin (grey) and ( c ′) synaptobrevin (yellow). ( c″ ) Merged. ( d – d ″) Lateral view of a different S. rosetta cell stained with antibodies against ( d ) tubulin and ( d ′) synaptobrevin. ( d ″) Merged. The dashed square in ( d ″) indicates to position of ( h ). ( e – e ″) A rosette colony of S. rosetta stained with the same antibodies as in ( c ). The orange arrows indicate a basal synaptobrevin signal. ( e ) Tubulin. ( e′ ) Synaptobrevin. ( e ″) Merged. The dotted square in ( e ″) indicates the position of ( f ). ( f ) Synaptobrevin-positive vesicles are in close contact with tubulin-positive cytoskeletal filaments. ( g ) TEM image showing the close contact between apical vesicles and tubulin filaments; av, apical vesicles; tf, tubulin filaments. ( h ) Image of a 3D reconstruction of the apical region of an S. rosetta cell. Apical vesicles are coloured in orange, tubulin filaments in light grey and the soma in half-transparent grey. Close contacts of vesicles and cytoskeletal filaments are indicated with white asterisks. The scale bar is 1 µm. Sros, Salpingoeca rosetta ; Hsap, Homo sapiens .

Article Snippet: Digital image stacks of the TEM sections of M. brevicollis and S. rosetta were imported into AMIRA (FEI Visualization Sciences Group) and aligned semi-manually.

Techniques: Sequencing, Staining

Journal: Philosophical Transactions of the Royal Society B: Biological Sciences

Article Title: Choanoflagellates and the ancestry of neurosecretory vesicles

doi: 10.1098/rstb.2019.0759

Figure Lengend Snippet: The diverse vesicular landscape of choanoflagellates. ( a ) Images of a 3D reconstruction of all vesicles in M. brevicollis (left) and S. rosetta (right). Individual vesicles are coloured randomly, and the cell is shown in half-transparent grey. A plot of all vesicle diameters measured is given in the middle. Mean diameters of different vesicle types are indicated by triangles in the same colours as in ( b–l ). ( b–f ) Visualization of separated vesicles of each vesicle type to show the localization within the soma of M. brevicollis . The Golgi-apparatus is shown in half-transparent lilac in ( b ). TEM images showing each vesicle type are given beneath images of the 3D model ( b′ – f′ ). ( g – k ) Visualization of separated vesicles of each vesicle type to show the localization within the soma of S. rosetta . The Golgi-apparatus is shown in half-transparent lilac in ( b ). TEM images showing each vesicle type are given beneath the 3D models ( g′ – k′ ). Scale bars of TEM images are 50 nm, scale bars of images of 3D reconstructions are approximately 250 nm. ( l ) Box and whiskers plots of the vesicle diameters within the different vesicle types (also see electronic supplementary material, table S2 and video S1 and S2). M. brevicollis : Golgi-associated vesicles (minimum: 37; median: 54; maximum: 79); small vesicles (minimum: 43; median 72; maximum 104); apical vesicles (minimum: 81; median: 109; maximum: 161); large extremely electron-lucent vesicles (minimum: 85; median: 132; maximum: 223); large electron-dense vesicles (minimum: 108; median 124; maximum 189). S. rosetta : Golgi-associated vesicles (minimum: 32; median: 55; maximum: 87); small vesicles (minimum: 51; median 78; maximum 116); apical vesicles (minimum: 102; median: 175; maximum: 233); large extremely electron-lucent vesicles (minimum: 153; median: 202; maximum: 301); medium vesicles (minimum: 107; median 125; maximum 180). M.bre, Monosiga brevicollis ; S.ros, Salpingoeca rosetta . nu = nucleus, ga = Golgi apparatus, ER = endoplasmic reticulum, mt = mitochondria, pm = plasma membrane.

Article Snippet: Digital image stacks of the TEM sections of M. brevicollis and S. rosetta were imported into AMIRA (FEI Visualization Sciences Group) and aligned semi-manually.

Techniques: Clinical Proteomics, Membrane