Journal: Nature Communications

Article Title: Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family

doi: 10.1038/s41467-022-32260-w

Figure Lengend Snippet: Schematic representations and electron microscope images of a N. elongata , b A. filiformis , c S. muelleri and d C. steedae . Rightmost panels display extracted sacculi (peptidoglycan) of respective Neisseriaceae . P proximal (host-attached) region of the cell, D distal region of the cell, OM outer membrane, PG peptidoglycan, CM cytoplasmic membrane. Scale bars correspond to 1 µm. The results are representative of at least three independent analyses.

Article Snippet: The bacterial strains Neisseria elongata subsp. elongata (DSM 17712), Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579), and Conchiformibius steedae (DSM 2580) were obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: Microscopy, Membrane

Journal: Nature Communications

Article Title: Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family

doi: 10.1038/s41467-022-32260-w

Figure Lengend Snippet: a Phase contrast image (left panel), corresponding epifluorescence image (middle panel) and enlarged selected regions (white frames in right panel) of A. filiformis consecutively labeled with HADA, BADA and TADA for 30 min, 15 min and 15 min, respectively. Asterisks point at newly completed septa and arrowheads point to nascent septa. Scale bars are 5 µm (middle panels) and 1 µm (right panels). b Septal fluorescence of HADA, BADA and TADA was plotted onto the long axis for two representative A. filiformis cells. Source data are provided as a Source Data file. c Schematic representation of A. filiformis growth mode. d Confocal images of A. filiformis consecutively labeled with HADA, BADA and TADA for 30 min, 15 min and 15 min, respectively. Asterisks point at newly completed septa and arrowheads point at nascent septa in a filament (left panel). Fluorescence emitted by a newly completed septum (septum 1 in white box in left panel) and by an incoming septum (septum 2 in white box in left panel) were rotated by 90° and are displayed in the middle and the right panels, respectively. Scale bar is 1 µm. e Schematic representation of A. filiformis growth mode. D distal, P proximal. The results are representative of at least three independent analyses.

Article Snippet: The bacterial strains Neisseria elongata subsp. elongata (DSM 17712), Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579), and Conchiformibius steedae (DSM 2580) were obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: Labeling, Fluorescence

Journal: Nature Communications

Article Title: Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family

doi: 10.1038/s41467-022-32260-w

Figure Lengend Snippet: The best evolutionary model for each partition was found by IQ-TREE version 1.6.3 and maximum-likelihood phylogenetic analysis was also performed using IQ-TREE using 10,000 ultrafast bootstrap replicates . Above the name of each species, scanning electron microscopy images display their morphology. Dark and light blue: coccoid Neisseriaceae ; green: rod-shaped Neisseriaceae ; red: multicellular longitudinally dividing (MuLDi) Neisseriaceae . Coccoid lineages 1 and 2 are indicated in blue. MuLDi lineages 1 and 2 are indicated in red. N.: Neisseria ; U.: Uruburuella ; S.: Simonsiella ; A.: Alysiella ; K.: Kingella ; C.: Conchiformibius ; S.: Snodgrassella ; V.: Vitreoscilla ; E.: Eikenella ; C.: Crenobacter . Crenobacter spp. served as out-group. In the absence of electron microscopy images, species’ morphology was defined as rod-shaped based on the reference strain describe in refs. for K. negevensis , for K. bonacorsii , for K. denitrificans , for E. longiqua and E. haliae , for Crenobacter luteus , for C. cavernae , for C. sedimenti , for C. intestine .

Article Snippet: The bacterial strains Neisseria elongata subsp. elongata (DSM 17712), Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579), and Conchiformibius steedae (DSM 2580) were obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: Electron Microscopy

Journal:

Article Title: Anti-Vpr Activity of a Yeast Chaperone Protein

doi: 10.1128/JVI.78.20.11016-11029.2004

Figure Lengend Snippet: Fission yeast strains, human cell lines, plasmids, and HIV-1 viral stocks

Article Snippet: All cells were normally grown at 30°C with constant shaking at 200 rpm unless otherwise specified. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strains, cell lines, plasmids, and viral stocks Genotype and characteristics Source or reference S. pombe strains SP223 Wild type, h − , ade6-216 , leu1-32 , ura4-294 ATCC Q812 Wild type, h − , leu1-32 , ura4-294 49 Q1649 Wild type, h − , leu1-32 , ura4-294 , gfp-hsp16 49 RE076 SP223 with single copy of F34I vpr integrated at ura4 locus; used for measuring Vpr-induced cell cycle G2 delay 19 RE007 SP223 with single copy of vpr integrated at ura4 locus; used for determining Vpr-induced cell killing This study RE078 SP223 with single copy of gfp-vpr integrated at ura4 locus; used for determining nuclear localization of Vpr This study Mammalian cell lines HeLa A cervical epithelial cell line ATCC H9 CD4+ cells derived from PBMC for high-yield permissive growth with HIV-1 44 CEM-SS CD4+ cells derived from human T4-lymphoblastoid cells 37 293T An embryonic kidney fibroblast cell line ATCC 293T-632 A 293T cell line expressing pVgRxR and pCMV-EBNA1 66 Plasmids pYZIN Fission yeast expression vector with an inducible nmt1 promoter and a leu1 selectable marker 63 pYZ3N Same as pYZ1N but with a 5′ GFP-tag 63 pSF173 Fission yeast expression vector with an inducible nmt1 promoter and a 5′ HA-tag, ura4 selectable ATCC pZY1 Mammalian expression vector with a muristerone A-inducible promoter; geneticin-resistant 66 pZH1 Mammalian expression vector with a muristerone A-inducible promoter; hygromycin-resistant 66 pCDNA3.1 Mammalian expression vector with a CMV promoter; hygromycin-resistant Invitrogen HIV-1 viral stocks HIV-1 LAI Vpr (+) HIV-1 viral laboratory (subtype B) strain LAI 4 HIV-1 NL4-3 Vpr (+) Vpr-positive NL4-3-based HIV-1 vector pNLHX 8 HIV-1 NL4-3 Vpr (−) Same as above; vpr gene is mutated at the start codon from ATG to GTG 43 HIV-1 (VSV-G) Vpr (+) Vpr-positive NL4-3-based HIV-1 vector.

Techniques: Derivative Assay, Expressing, Plasmid Preparation, Marker

Journal: bioRxiv

Article Title: Stable chromosome configuration and loop-based polarization in animal symbionts

doi: 10.1101/2023.12.21.572873

Figure Lengend Snippet: Schematic representations and confocal microscope images of C. steedae (a), A. filiformis (b) and S. muelleri labeled with the peptidoglycan precursor TADA for 60 min (green) and stained with Hoechst 33342 (magenta). (a) Viewed from the top, C. steedae DNA is either homogenously distributed (cell #1), excluded from midcell (cell #2) or X-shaped in cells undergoing late septation stages (cell #3). Rightmost panel displays a side view of cells 1-3. (b) Frontal view of an A. filiformis filament reveals a V-shaped DNA localization pattern. Rightmost panel displays a 90 degrees rotated view of the cells marked with an asterisk. (c) Viewed from the top , S. muelleri DNA is either excluded from midcell (cell #1), displaying a X-shaped pattern in cells undergoing late septation stages (cell #2) or homogenously distributed (cell #3). Rightmost panel displays a side view of cells 1-3. Scale bars are 1 µm.

Article Snippet: The bacterial strains Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579) and Conchiformibius steedae (DSM 2580) have been received from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: Microscopy, Labeling, Staining

Journal: bioRxiv

Article Title: Stable chromosome configuration and loop-based polarization in animal symbionts

doi: 10.1101/2023.12.21.572873

Figure Lengend Snippet: (a, j) Histograms showing number of ori or (d,j) ter foci per cell. Confocal microscope images of representative filaments of C. steedae (b,e) and S. muelleri (h,k) subjected to either ori DNA FISH (b,h) or ter DNA FISH (e,k); phase contrast images are displayed in upper panels and corresponding FISH (green) and DNA (magenta) fluorescence images in bottom panels. (c,i) Subcellular localization of 215 ori foci in C. steedae and of 188 ori foci in S. muelleri . (f, j) Subcellular localization of 236 ter foci in C. steedae cells and of 293 ter foci in S. muelleri . (m) Model of ori-ter-ter-ori chromosome configuration and lateral chromosome segregation in the diploid crescent-shaped S. muelleri and C. steedae . Scale bars are 1 µm.

Article Snippet: The bacterial strains Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579) and Conchiformibius steedae (DSM 2580) have been received from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: Microscopy, Fluorescence

Journal: bioRxiv

Article Title: Stable chromosome configuration and loop-based polarization in animal symbionts

doi: 10.1101/2023.12.21.572873

Figure Lengend Snippet: (a, b, c) ori -centered contact maps (green arrows denote ori ), (d) dif -centered S. muelleri contact map (red arrows denote dif ) of cells grown on solid medium, highlighting the loops observed in both replicates (black circles) in the lower half of each contact map. Below each map, the black or red circles show the position of highly expressed genes (HEGs) and rRNA operons if their presence correlates with a CID border. Below each track, the Frontier Index (FI) shows frontiers with upstream (green) or downstream (orange) bias of interaction and the normalized RNA-Seq counts in 5 kb bins show the transcriptomic data obtained in the same conditions that the contact map. The dashed line represents the threshold use to identify highly expressed regions. (e) Detail of (a) showing the A. filiformis loop right of ori . (f) Detail of (c) showing the S. muelleri ori region (left panel) and detail of (c) showing corner peaks of CIDs (right panel). (g) Detail of (d) showing the S. muelleri region around dif , with CID borders. The remaining replicates are shown in Supplementary Figs. 6-8.

Article Snippet: The bacterial strains Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579) and Conchiformibius steedae (DSM 2580) have been received from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: RNA Sequencing

Journal: bioRxiv

Article Title: Stable chromosome configuration and loop-based polarization in animal symbionts

doi: 10.1101/2023.12.21.572873

Figure Lengend Snippet: (a, b) Circular representation of the A. filiformis and S. muelleri chromosomes when grown on solid medium (top panels) or in liquid medium (bottom panels), respectively. Looping regions are indicated as black lines on the white circle. The three inner colored circles represent the position of genes classified as one of the three COG categories ‘Cellular Processes and Signaling’ (red), ‘Information Storage and Processing’ (blue), and ‘Metabolism’ (green). Connections between looping regions (loops) are shown in black. Green arrows indicate the position of ori , and the red arrows indicate the position of dif .

Article Snippet: The bacterial strains Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579) and Conchiformibius steedae (DSM 2580) have been received from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques:

Journal: bioRxiv

Article Title: Stable chromosome configuration and loop-based polarization in animal symbionts

doi: 10.1101/2023.12.21.572873

Figure Lengend Snippet: (a, b, c) ori -centered contact maps (green arrows denote ori ), highlighting the loops observed in both replicates (black circles) in the lower half of each contact map. Below each map, the black or red circles show the position of highly expressed genes (HEGs) and rRNA operons if their presence correlates with a CID border. Below each track, the Frontier Index (FI) shows frontiers with upstream (green) or downstream (orange) bias of interaction and the normalized RNA-Seq counts in 5 kb bins show the transcriptomic data obtained in the same conditions that the contact map. The dashed line represents the threshold use to identify highly expressed regions. (d) Detail of (b) showing the absence of the loop shown in (dashed circle) and the emergence of a new loop containing the ori (closed circle). (e) Detail of (c) showing the absence of many loops (dashed circles) and the emergence of six loops (closed circles) in the vicinity of S. muelleri ori. (f) Detail of (c) showing the absence of the two corner peaks shown in (right panel).

Article Snippet: The bacterial strains Alysiella filiformis (DSM 16848), Simonsiella muelleri (DSM 2579) and Conchiformibius steedae (DSM 2580) have been received from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ).

Techniques: RNA Sequencing

Journal: Frontiers in Microbiology

Article Title: Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

doi: 10.3389/fmicb.2016.01330

Figure Lengend Snippet: Physiological and biochemical characteristics of (1) strain PCO and its phylogenetic related species: (2) Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), (3) T. brockii subsp. finnii (DSM 3389 T ), (4) T. pseudethanolicus (DSM 2355 T ), and (5) T. wiegelii (DSM 10319 T ) .

Article Snippet: Type strains of Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), T. brockii subsp. finnii (DSM 3389 T ), T. pseudethanolicus (DSM 2355 T ), and T. wiegelii (DSM 10319 T ) were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ; German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).

Techniques: Starch

Journal: Frontiers in Microbiology

Article Title: Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

doi: 10.3389/fmicb.2016.01330

Figure Lengend Snippet: Glucose conversion, production of H 2 from glucose and growth curves over time by (A) strain PCO, (B) Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), (C) T. brockii subsp. finnii (DSM 3389 T ), (D) T . pseudethanolicus (DSM 2355 T ), and (E) T. wiegelii (DSM 10319 T ), in incubations with different CO concentration in the gas phase (0, 25, 50, 75, or 100% CO) . Plotted are the average data of duplicate experiments. The values of optical density were plotted vs. time on a logarithmic scale.

Article Snippet: Type strains of Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), T. brockii subsp. finnii (DSM 3389 T ), T. pseudethanolicus (DSM 2355 T ), and T. wiegelii (DSM 10319 T ) were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ; German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).

Techniques: Concentration Assay

Journal: Frontiers in Microbiology

Article Title: Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

doi: 10.3389/fmicb.2016.01330

Figure Lengend Snippet: Production of ethanol and organic acids (lactate and acetate) from glucose, over time, by (A) strain PCO, (B) Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), (C) T. brockii subsp. finnii (DSM 3389 T ), (D) T . pseudethanolicus (DSM 2355 T ), and (E) T. wiegelii (DSM 10319 T ), in incubations with different CO concentration in the gas phase (0, 25, 50, 75, or 100% CO) . Plotted are the average data of duplicate experiments.

Article Snippet: Type strains of Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), T. brockii subsp. finnii (DSM 3389 T ), T. pseudethanolicus (DSM 2355 T ), and T. wiegelii (DSM 10319 T ) were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ; German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).

Techniques: Concentration Assay

Journal: Frontiers in Microbiology

Article Title: Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

doi: 10.3389/fmicb.2016.01330

Figure Lengend Snippet: Effect of CO partial pressure on glucose conversion and carbon recovery (%) by strain PCO, Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), T. brockii subsp. finnii (DSM 3389 T ), T. pseudethanolicus (DSM 2355 T ), and T. wiegelii (DSM 10319 T ) .

Article Snippet: Type strains of Thermoanaerobacter thermohydrosulfuricus (DSM 527 T ), T. brockii subsp. finnii (DSM 3389 T ), T. pseudethanolicus (DSM 2355 T ), and T. wiegelii (DSM 10319 T ) were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ; German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).

Techniques: Produced