spheroidsizer Search Results


rhodobacter sphaeroides atcc 49419  (ATCC)
91
ATCC rhodobacter sphaeroides atcc 49419
Rhodobacter Sphaeroides Atcc 49419, supplied by ATCC, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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non-cell adhesive 96-well culture plate  (Sumilon Polyester)
90
Sumilon Polyester non-cell adhesive 96-well culture plate
Non Cell Adhesive 96 Well Culture Plate, supplied by Sumilon Polyester, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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t-25 ultra-low attachment microcavity flasks  (Corning Life Sciences)
90
Corning Life Sciences t-25 ultra-low attachment microcavity flasks
T 25 Ultra Low Attachment Microcavity Flasks, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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shtns4 spheroids  (Verlag GmbH)
90
Verlag GmbH shtns4 spheroids
Shtns4 Spheroids, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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autologous chondrocytic spheroids  (CO.DON AG)
90
CO.DON AG autologous chondrocytic spheroids
Autologous Chondrocytic Spheroids, supplied by CO.DON AG, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rhodobacter sphaeroides 2 4 1  (ATCC)
95
ATCC rhodobacter sphaeroides 2 4 1
A literature survey of the relationship between the presence of the luxS gene and QS-2 dependent behavior in bacterial species carrying either a luxP - or a lsrB -gene homolog in their genome
Rhodobacter Sphaeroides 2 4 1, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cyanothece sp  (ATCC)
96
ATCC cyanothece sp
Gene content in, and downstream of, the nif gene region of <t>Cyanothece</t> sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.
Cyanothece Sp, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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se45 rhodobacter sphaeroides atcc 17029 ruegeria mobilis f1926 sulfitobacter sp  (ATCC)
95
ATCC se45 rhodobacter sphaeroides atcc 17029 ruegeria mobilis f1926 sulfitobacter sp
Gene content in, and downstream of, the nif gene region of <t>Cyanothece</t> sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.
Se45 Rhodobacter Sphaeroides Atcc 17029 Ruegeria Mobilis F1926 Sulfitobacter Sp, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rhodobacter sphaeroides 2 4 1 nc 007493  (ATCC)
90
ATCC rhodobacter sphaeroides 2 4 1 nc 007493
Gene content in, and downstream of, the nif gene region of <t>Cyanothece</t> sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.
Rhodobacter Sphaeroides 2 4 1 Nc 007493, supplied by ATCC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rhodobacter sphaeroides atcc 17025 gfa q92wx6  (ATCC)
95
ATCC rhodobacter sphaeroides atcc 17025 gfa q92wx6
Gene content in, and downstream of, the nif gene region of <t>Cyanothece</t> sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.
Rhodobacter Sphaeroides Atcc 17025 Gfa Q92wx6, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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spheroids  (Merck & Co)
86
Merck & Co spheroids
Gene content in, and downstream of, the nif gene region of <t>Cyanothece</t> sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.
Spheroids, supplied by Merck & Co, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


A literature survey of the relationship between the presence of the luxS gene and QS-2 dependent behavior in bacterial species carrying either a luxP - or a lsrB -gene homolog in their genome

Journal: BMC Microbiology

Article Title: Lack of genomic evidence of AI-2 receptors suggests a non-quorum sensing role for luxS in most bacteria

doi: 10.1186/1471-2180-8-154

Figure Lengend Snippet: A literature survey of the relationship between the presence of the luxS gene and QS-2 dependent behavior in bacterial species carrying either a luxP - or a lsrB -gene homolog in their genome

Article Snippet: 97-27 (NC_005957), Bacillus weihenstephanensis KBAB4 (NC_010184), Bifidobacterium adolescentis (NC_008618), Bifidobacterium longum (NZ_AABM02000006), Borrelia burgdorferi (NC_001318), Campylobacter jejuni (NC_003912), Clostridium acetobutylicum (NC_003030), Clostridium difficile (NC_009089), Clostridium perfringens (NC_008262) , Desulfovibrio desulfuricans (NC_007519), Desulfuromonas acetoxidans (NZ_AAEW00000000), Erwinia amylovora (genome project for strain Ea273 , Erwinia carotovora subsp. atroseptica SCRI1043 (NC_004547), Escherichia coli (NC_000913), Haemophilus influenzae (NZ_AADO01000002), Haemophilus somnus (NZ_AACJ01000020), Helicobacter pylori (NC_008086), Klebsiella pneumoniae (genome project for strain MGH 78578, , Listeria monocytogenes (NC_002973), Mannheimia succiniciproducens (NC_006300), Neisseria meningiditis (NC_008767), Pasteurella multocida (NC_002663), Photobacterium profundum (NC_006370), Photorhabdus luminescens (NC_005126), Rhodobacter sphaeroides 2.4.1 (NC_007493-94), Rhodobacter sphaeroides ATCC 17025 (NC_009428), Rhodobacter sphaeroides ATCC 17029 (NC_009049-50), Salmonella bongori (genome project for strain 12419 ATCC 43975, , Salmonella enterica (NC_006905), Salmonella typhimurium (NC_003197), Serratia marcescens (genome project for strain Db11 ), Shewanella oneidensis MC_1 (NC_004347), Shighella boydii (NZ_AAKA01000004), Shighella dysenteriae (NZ_AAMJ01000009), Shighella flexneri (NC_004337), Shighella sonnei (NC_007384), Sinorrhizobium meliloti (NC_003078), Sodalis glossinidius (NC_007712), Staphylococcus aureus (NC_003923), Streptococcus pyogenes (NC_003485), Vibrio angustum (NZ_AAOJ00000000), Vibrio cholerae (NC_002505), Vibrio fischeri (NC_006840), Vibrio harveyi (NC_009783-NC_009784), Vibrio vulnificus (NC_004459), Xenorhabdus sp. (genome project for X. nematophila ATCC 19061 and X. bovienii , , Yersinia bercovieri (NZ_AALC00000000), Yersinia enterocolitica (NC_008800), Yersinia frederiksenii (NZ_AALE01000042), Yersinia intermedia (NZ_AALF01000074), Yersinia mollaretii (NZ_AALD01000064), Yersinia pestis (NC_004088), Yersinia pseudotubercolosis (NC_006155).

Techniques:

Comparison of the operons coding for the Lsr-like receptors in the luxS -negative α-proteobacteria R. sphaeroides 2.4.1 and S. meliloti 1021 with the lsr cluster of AI-2 producers S. typhimurium and E. coli K12 . The lsr -like operons are located on the highly variable chromosome II of R. sphaeroides 2.4.1 (accession number NC_007494) and on the pSymB megaplasmid of S. meliloti 1021 (NC_003078) respectively. The transporter core is composed of a periplasmic AI-2 binding protein (LsrB), two hydrophobic proteins which for an homodimeric transmembrane channel (LsrC and LsrD) and a hydrophilic ATP-binding protein (LsrA). The expression of the lsr operon is controlled by repressor protein LsrR and AI-2 kinase LsrK which is responsible for the production of phospho-AI-2, the lsr operon inducer. In S. typhimurium (NC_003197), the LsrF and LsrG proteins are involved in modifying phospho-AI-2 . For comparison ribose and xylose ABC transporters of E. coli K12 (NC_000913) are shown below. Proteins with the same function are coded with the same color. As point of reference, locus tags for selected genes are marked inside the arrows.

Journal: BMC Microbiology

Article Title: Lack of genomic evidence of AI-2 receptors suggests a non-quorum sensing role for luxS in most bacteria

doi: 10.1186/1471-2180-8-154

Figure Lengend Snippet: Comparison of the operons coding for the Lsr-like receptors in the luxS -negative α-proteobacteria R. sphaeroides 2.4.1 and S. meliloti 1021 with the lsr cluster of AI-2 producers S. typhimurium and E. coli K12 . The lsr -like operons are located on the highly variable chromosome II of R. sphaeroides 2.4.1 (accession number NC_007494) and on the pSymB megaplasmid of S. meliloti 1021 (NC_003078) respectively. The transporter core is composed of a periplasmic AI-2 binding protein (LsrB), two hydrophobic proteins which for an homodimeric transmembrane channel (LsrC and LsrD) and a hydrophilic ATP-binding protein (LsrA). The expression of the lsr operon is controlled by repressor protein LsrR and AI-2 kinase LsrK which is responsible for the production of phospho-AI-2, the lsr operon inducer. In S. typhimurium (NC_003197), the LsrF and LsrG proteins are involved in modifying phospho-AI-2 . For comparison ribose and xylose ABC transporters of E. coli K12 (NC_000913) are shown below. Proteins with the same function are coded with the same color. As point of reference, locus tags for selected genes are marked inside the arrows.

Article Snippet: 97-27 (NC_005957), Bacillus weihenstephanensis KBAB4 (NC_010184), Bifidobacterium adolescentis (NC_008618), Bifidobacterium longum (NZ_AABM02000006), Borrelia burgdorferi (NC_001318), Campylobacter jejuni (NC_003912), Clostridium acetobutylicum (NC_003030), Clostridium difficile (NC_009089), Clostridium perfringens (NC_008262) , Desulfovibrio desulfuricans (NC_007519), Desulfuromonas acetoxidans (NZ_AAEW00000000), Erwinia amylovora (genome project for strain Ea273 , Erwinia carotovora subsp. atroseptica SCRI1043 (NC_004547), Escherichia coli (NC_000913), Haemophilus influenzae (NZ_AADO01000002), Haemophilus somnus (NZ_AACJ01000020), Helicobacter pylori (NC_008086), Klebsiella pneumoniae (genome project for strain MGH 78578, , Listeria monocytogenes (NC_002973), Mannheimia succiniciproducens (NC_006300), Neisseria meningiditis (NC_008767), Pasteurella multocida (NC_002663), Photobacterium profundum (NC_006370), Photorhabdus luminescens (NC_005126), Rhodobacter sphaeroides 2.4.1 (NC_007493-94), Rhodobacter sphaeroides ATCC 17025 (NC_009428), Rhodobacter sphaeroides ATCC 17029 (NC_009049-50), Salmonella bongori (genome project for strain 12419 ATCC 43975, , Salmonella enterica (NC_006905), Salmonella typhimurium (NC_003197), Serratia marcescens (genome project for strain Db11 ), Shewanella oneidensis MC_1 (NC_004347), Shighella boydii (NZ_AAKA01000004), Shighella dysenteriae (NZ_AAMJ01000009), Shighella flexneri (NC_004337), Shighella sonnei (NC_007384), Sinorrhizobium meliloti (NC_003078), Sodalis glossinidius (NC_007712), Staphylococcus aureus (NC_003923), Streptococcus pyogenes (NC_003485), Vibrio angustum (NZ_AAOJ00000000), Vibrio cholerae (NC_002505), Vibrio fischeri (NC_006840), Vibrio harveyi (NC_009783-NC_009784), Vibrio vulnificus (NC_004459), Xenorhabdus sp. (genome project for X. nematophila ATCC 19061 and X. bovienii , , Yersinia bercovieri (NZ_AALC00000000), Yersinia enterocolitica (NC_008800), Yersinia frederiksenii (NZ_AALE01000042), Yersinia intermedia (NZ_AALF01000074), Yersinia mollaretii (NZ_AALD01000064), Yersinia pestis (NC_004088), Yersinia pseudotubercolosis (NC_006155).

Techniques: Comparison, Binding Assay, Expressing

Gene content in, and downstream of, the nif gene region of Cyanothece sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Gene content in, and downstream of, the nif gene region of Cyanothece sp. ATCC 51142 and spheroid body of R. gibba . Blue and red bars represent orfs coded on the leading or lagging strand of DNA, respectively. The locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. fdx N*); B) Gene deletion with DNA loss (e.g. cyl 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. cyl 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. cyl 0019). See text for further description of individual modifications.

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques:

Genome features of obligate intracellular symbiotic and parasitic bacteria

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Genome features of obligate intracellular symbiotic and parasitic bacteria

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques:

Analysis of Ferredoxin N . A . Multiple alignment of cyanobacterial FdxN proteins. Accession numbers: CyaATCC51142: AAW56985.1 ( Cyanothece sp. ATVV51142); CyaPCC8801: AAC33373.1 ( Cyanothece sp. PCC8801 ); CyaCCY0110: ZP_01727762.1 ( Cyanothece sp. CCY0110 ); GloeK068DGA: BAF47148.1 ( Gloeothece sp. KO68DGA ); NostPCC7120: AAA22005.1 ( Nostoc punctiforme PCC 7120); AnabATCC29413: YP_324413.1 ( Anabaena variabilis ATCC 29413 ). B . Alignment of Cyanothece sp. ATCC51142 FdxN protein with the spheroid body fdxN* pseudogene translated in 3 forward reading frames. Evidence of homology, at the level of amino acid similarity, is distributed across all 3 reading frames of the pseudogene, indicating multiple substitutions and single nucleotide deletion events.

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Analysis of Ferredoxin N . A . Multiple alignment of cyanobacterial FdxN proteins. Accession numbers: CyaATCC51142: AAW56985.1 ( Cyanothece sp. ATVV51142); CyaPCC8801: AAC33373.1 ( Cyanothece sp. PCC8801 ); CyaCCY0110: ZP_01727762.1 ( Cyanothece sp. CCY0110 ); GloeK068DGA: BAF47148.1 ( Gloeothece sp. KO68DGA ); NostPCC7120: AAA22005.1 ( Nostoc punctiforme PCC 7120); AnabATCC29413: YP_324413.1 ( Anabaena variabilis ATCC 29413 ). B . Alignment of Cyanothece sp. ATCC51142 FdxN protein with the spheroid body fdxN* pseudogene translated in 3 forward reading frames. Evidence of homology, at the level of amino acid similarity, is distributed across all 3 reading frames of the pseudogene, indicating multiple substitutions and single nucleotide deletion events.

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques:

Truncation of nif U in spheroid bodies . A . GATA plot for Cyanothece and spheroid body nif U indicating conserved regions. GATaligner settings: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 92.0. GATAPlotter score settings: Max: 141 bits, expect 9E-38; Min: 28 bits, expect 9E-4. GATAPlotter scores are indicated. B . Multiple alignment of predicted amino acid sequences for NifU indicating an N-terminal truncation in the homologue from the endosymbiont. NifU accession numbers: Cya51142: AAW56987.1 ( Cyanothece sp. ATCC 51142); Cya0110: ZP_01727764.1 ( Cyanothece sp. CCY0110); GloKO68DGA: BAF47150.1 ( Gloeothece sp. KO68DGA); Cya8801: AAC33371.1 ( Cyanothece sp. PCC 8801); Lyn8106: ZP_01620769.1 ( Lyngbya sp. PCC 8106); TriIMS101: AAF82636.1 ( Trichodesmium sp. IMS101); NdCCY9414: ZP_01628437.1 ( Nodularia spumigena CCY9414); Nos73102: ZP_00112317.1 ( Nostoc punctiforme PCC 73102); SynJA2: YP_476679.1 ( Synechococcus sp. JA-2-3B'a(2–13)); sb8: AAW57048.1 (spheroid body); Syn6803: NP_442853.1 ( Synechocystis sp. PCC6803); Glo7421: NP_925823.1 ( Gloeobacter violaceus PCC 7421); Cro8501: ZP_00516385.1 ( Crocosphaera watsonii WH 8501).

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Truncation of nif U in spheroid bodies . A . GATA plot for Cyanothece and spheroid body nif U indicating conserved regions. GATaligner settings: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 92.0. GATAPlotter score settings: Max: 141 bits, expect 9E-38; Min: 28 bits, expect 9E-4. GATAPlotter scores are indicated. B . Multiple alignment of predicted amino acid sequences for NifU indicating an N-terminal truncation in the homologue from the endosymbiont. NifU accession numbers: Cya51142: AAW56987.1 ( Cyanothece sp. ATCC 51142); Cya0110: ZP_01727764.1 ( Cyanothece sp. CCY0110); GloKO68DGA: BAF47150.1 ( Gloeothece sp. KO68DGA); Cya8801: AAC33371.1 ( Cyanothece sp. PCC 8801); Lyn8106: ZP_01620769.1 ( Lyngbya sp. PCC 8106); TriIMS101: AAF82636.1 ( Trichodesmium sp. IMS101); NdCCY9414: ZP_01628437.1 ( Nodularia spumigena CCY9414); Nos73102: ZP_00112317.1 ( Nostoc punctiforme PCC 73102); SynJA2: YP_476679.1 ( Synechococcus sp. JA-2-3B'a(2–13)); sb8: AAW57048.1 (spheroid body); Syn6803: NP_442853.1 ( Synechocystis sp. PCC6803); Glo7421: NP_925823.1 ( Gloeobacter violaceus PCC 7421); Cro8501: ZP_00516385.1 ( Crocosphaera watsonii WH 8501).

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques:

Spheroid body orf sbl 0010 encodes a fusion protein derived from homologues of the Cyanothece sp. ATCC51142 Cyl0018 and Cyl0020 proteins . A . Alignment of predicted amino acid sequences for spheroid body protein Sbl0010 and Cyanothece proteins Cyl0018 and Cyl0020. Deletion in the endosymbiont genome of cyl 0019 in the creation of sbl 0010 can be inferred during reductive genome evolution. In Sb10010, homologues of Cyl0018 and Cyl0020 have been conserved in full length and are separated by a 17 amino acid residues. Cyl0018: green, Cyl0020: orange, Sbl0010: black. B . Cyl0018 and Cyl0020 are highly conserved in cyanobacteria closely related to the spheroid body. They are aseparated by 1–5 genes when they co-occur at the same locus, but in some cases they are encoded at different loci of the genome (indicated by x).

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Spheroid body orf sbl 0010 encodes a fusion protein derived from homologues of the Cyanothece sp. ATCC51142 Cyl0018 and Cyl0020 proteins . A . Alignment of predicted amino acid sequences for spheroid body protein Sbl0010 and Cyanothece proteins Cyl0018 and Cyl0020. Deletion in the endosymbiont genome of cyl 0019 in the creation of sbl 0010 can be inferred during reductive genome evolution. In Sb10010, homologues of Cyl0018 and Cyl0020 have been conserved in full length and are separated by a 17 amino acid residues. Cyl0018: green, Cyl0020: orange, Sbl0010: black. B . Cyl0018 and Cyl0020 are highly conserved in cyanobacteria closely related to the spheroid body. They are aseparated by 1–5 genes when they co-occur at the same locus, but in some cases they are encoded at different loci of the genome (indicated by x).

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques: Derivative Assay

A/T-G/C frequencies in Cyanothece sp. ATCC 51142 and spheroid body genome fragments . A/T-G/C-plot for the genome region shown in Fig. 1 (red: AT; blue:G/C), indicating a high AT composition in the large non-coding regions (black arrows) of the spheroid body fragment.

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: A/T-G/C frequencies in Cyanothece sp. ATCC 51142 and spheroid body genome fragments . A/T-G/C-plot for the genome region shown in Fig. 1 (red: AT; blue:G/C), indicating a high AT composition in the large non-coding regions (black arrows) of the spheroid body fragment.

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques:

PCR analysis of missing or pseudogenisised genes . PCR analysis of Cyanothece sp. ATCC 51142 (CY), R. gibba (RG) and spheroid body (SB) DNA. Amplification with primers specific for the cyanobacterial fdx N, pet J, psb C, cyl 0012 and cyl 0017 genes show that the analysed genes are not encoded in R. gibba and the endosymbiont's genome. CYrecF and SBrecF were used as positive controls. GeneRuler™ Express DNA Ladder (Fermentas) was used as molecular weight standard.

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: PCR analysis of missing or pseudogenisised genes . PCR analysis of Cyanothece sp. ATCC 51142 (CY), R. gibba (RG) and spheroid body (SB) DNA. Amplification with primers specific for the cyanobacterial fdx N, pet J, psb C, cyl 0012 and cyl 0017 genes show that the analysed genes are not encoded in R. gibba and the endosymbiont's genome. CYrecF and SBrecF were used as positive controls. GeneRuler™ Express DNA Ladder (Fermentas) was used as molecular weight standard.

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques: DNA Amplification, Molecular Weight

Pairwise alignments for RecA and for RecF . Alignment of RecA (left) and RecF (right) homologues from the spheroid body (SB) and Cyanothece sp . ATCC51142 (CY) genomes. The spheroid body encodes complete full length rec A and rec F orfs .

Journal: BMC Evolutionary Biology

Article Title: The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

doi: 10.1186/1471-2148-8-30

Figure Lengend Snippet: Pairwise alignments for RecA and for RecF . Alignment of RecA (left) and RecF (right) homologues from the spheroid body (SB) and Cyanothece sp . ATCC51142 (CY) genomes. The spheroid body encodes complete full length rec A and rec F orfs .

Article Snippet: In order to investigate this, we have constructed fosmid libraries of the spheroid body and Cyanothece sp. ATCC 51142 and analysed genomic regions of special interest.

Techniques: