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Sam Pitluck - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of planctomyces brasiliensis type strain dsm 5305t phylogenomic analysis and reclassification of planctomycetes including the descriptions of gimesia gen nov planctopirus gen nov and rubinisphaera gen nov and emended descript
Standards in Genomic Sciences, 2014Co-Authors: Carmen Scheuner, Jan-fang Cheng, Lynne Goodwin, Matt Nolan, Brian J Tindall, Megan Lu, Alla Lapidus, Sam PitluckAbstract:Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal Cell Compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother Cell and a Cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
Megan Lu - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of planctomyces brasiliensis type strain dsm 5305t phylogenomic analysis and reclassification of planctomycetes including the descriptions of gimesia gen nov planctopirus gen nov and rubinisphaera gen nov and emended descript
Standards in Genomic Sciences, 2014Co-Authors: Carmen Scheuner, Jan-fang Cheng, Lynne Goodwin, Matt Nolan, Brian J Tindall, Megan Lu, Alla Lapidus, Sam PitluckAbstract:Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal Cell Compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother Cell and a Cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
Lynne Goodwin - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of planctomyces brasiliensis type strain dsm 5305t phylogenomic analysis and reclassification of planctomycetes including the descriptions of gimesia gen nov planctopirus gen nov and rubinisphaera gen nov and emended descript
Standards in Genomic Sciences, 2014Co-Authors: Carmen Scheuner, Jan-fang Cheng, Lynne Goodwin, Matt Nolan, Brian J Tindall, Megan Lu, Alla Lapidus, Sam PitluckAbstract:Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal Cell Compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother Cell and a Cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
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Standards in Genomic Sciences (2010) 3:47-56 DOI:10.4056/sigs.1052813 Complete genome sequence of Planctomyces limnophilus
2014Co-Authors: Type Strain T, Susanne Schneider, Hope Tice, Jan-fang Cheng, Susan Lucas, Kurt Labutti, Johannes Sikorski, Matt Nolan, Glavina Del Rio, Lynne GoodwinAbstract:Planctomyces limnophilus Hirsch and Müller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal Cell Compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother Cell and a Cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its Cell shape and size, the formation of multiCellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project
Nancy H Ruddle - One of the best experts on this subject based on the ideXlab platform.
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prevention of diabetes by fty720 mediated stabilization of peri islet tertiary lymphoid organs
Diabetes, 2010Co-Authors: Cristina Penaranda, Nancy H Ruddle, Qizhi Tang, Jeffrey A BluestoneAbstract:OBJECTIVE The nonobese diabetic (NOD) mouse is a well-established mouse model of spontaneous type 1 diabetes, which is characterized by an autoimmune destruction of the insulin-secreting pancreatic β-Cells. In this study, we address the role of tertiary lymphoid organs (TLOs) that form in the pancreas of NOD mice during disease progression. METHODS We developed a model designed to “lock” lymphocytes in the pancreatic lymph node (PLN) and pancreas by the use of FTY720, which blocks the exit of lymphocytes from lymph nodes. A combination of flow cytometry, immunofluorescence, and analysis of clinical scores was used to study the effects of long-term FTY720 treatment on TLO development and development of diabetes. RESULTS Continuous treatment of NOD mice with FTY720 prevented diabetes development even at a time of significant insulitis. Treatment withdrawal led to accelerated disease independent of the PLN. Interestingly, naive T-Cells trafficked to and proliferated in the TLOs. In addition, morphological changes were observed that occurred during the development of the disease. Remarkably, although the infiltrates are not organized into T/B-Cell compartments in 8-week-old mice, by 20 weeks of age, and in age-matched mice undergoing FTY720 treatment, the infiltrates showed a high degree of organization. However, in naturally and FTY720-induced diabetic mice, T/B-Cell Compartmentalization was lost. CONCLUSION Our data show that TLOs are established during diabetes development and suggest that islet destruction is due to a loss of TLO integrity, which may be prevented by FTY720 treatment.
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lymphotoxin plays a crucial role in the development and function of nasal associated lymphoid tissue through regulation of chemokines and peripheral node addressin
American Journal of Pathology, 2005Co-Authors: Xiaoyan Ying, K Chan, Priti Shenoy, Myriam Hill, Nancy H RuddleAbstract:The mechanism of nasal-associated lymphoid tissue (NALT) development is incompletely understood with regard to the roles of cytokines, chemokines, and vascular addressins. Development of the wild-type NALT continued in the immediate postnatal period with gradual increases in Cellularity, Compartmentalization into T- and B-Cell zones, and expression of lymphotoxin (LT)-α, LT-β, and lymphoid chemokines (CCL21, CCL19, CXCL13). High endothelial venules (HEVs) developed that expressed GlyCAM-1, HEC-6ST [an enzyme crucial for expression of luminal peripheral node addressin (PNAd)], and PNAd itself. LT-β −/− and LT-α −/− NALTs had fewer Cells than those of wild-type mice, reduced (LT-β −/− ) or absent (LT-α −/− ) lymphoid chemokines, and no T- and B-Cell Compartmentalization. LT-β −/− HEVs expressed only abluminal PNAd and no HEC-6ST or GlyCAM-1. LT-α −/− HEVs had no PNAd, HEC-6ST, or GlyCAM-1. Because intranasal immunization gives rise to vaginal IgA, immunization of LT-β −/− mice, which retain cervical lymph nodes, might generate such a response. Intranasal immunization with ovalbumin and cholera toxin revealed lower cytokine levels in the LT-α −/− and LT-β −/− NALTs, and undetectable vaginal IgA. In contrast, splenic cytokines and serum IgG titers, although reduced, were detectable. These data indicate that LT-α 3 and LT-α 1 β 2 cooperatively contribute to NALT development and function through regulation of lymphoid chemokines and adhesion molecules; they are the first to implicate LT-α 1 β 2 in GlyCAM-1 regulation in NALT HEV development.
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ectopic ltαβ directs lymphoid organ neogenesis with concomitant expression of peripheral node addressin and a hev restricted sulfotransferase
Journal of Experimental Medicine, 2003Co-Authors: Danielle L Drayton, Xiaoyan Ying, Jason Lee, Werner Lesslauer, Nancy H RuddleAbstract:Lymph node (LN) function depends on T and B Cell Compartmentalization, antigen presenting Cells, and high endothelial venules (HEVs) expressing mucosal addressin Cell adhesion molecule (MAdCAM-1) and peripheral node addressin (PNAd), ligands for naive Cell entrance into LNs. Luminal PNAd expression requires a HEV-restricted sulfotransferase (HEC-6ST). To investigate LTαβ's activities in lymphoid organogenesis, mice simultaneously expressing LTα and LTβ under rat insulin promoter II (RIP) control were compared with RIPLTα mice in a model of lymphoid neogenesis and with LTβ−/− mice. RIPLTαβ pancreata exhibited massive intra-islet mononuclear infiltrates that differed from the more sparse peri-islet Cell accumulations in RIPLTα pancreata: separation into T and B Cell areas was more distinct with prominent FDC networks, expression of lymphoid chemokines (CCL21, CCL19, and CXCL13) was more intense, and L-selectin+ Cells were more frequent. In contrast to the predominant abluminal PNAd pattern of HEV in LTβ−/− MLN and RIPLTα pancreatic infiltrates, PNAd was expressed at the luminal and abluminal aspects of HEV in wild-type LN and in RIPLTαβ pancreata, coincident with HEC-6ST. These data highlight distinct roles of LTα and LTαβ in lymphoid organogenesis supporting the notion that HEC-6ST–dependent luminal PNAd is under regulation by LTαβ.
John A Fuerst - One of the best experts on this subject based on the ideXlab platform.
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Cell Compartmentalization and endocytosis in planctomycetes structure and function in complex bacteria
2013Co-Authors: John A Fuerst, Richard I Webb, Evgeny SagulenkoAbstract:Planctomycetes are unique among the domain Bacteria in possessing Cells with a complex plan defined by internal membranes forming separated compartments within the Cell. They also possess other unique features such as Cell walls composed of protein as a major polymer instead of the peptidoglycan typical of other bacteria. All species examined display an underlying shared Cell organization in which an internal intracytoplasmic membrane separates two major Cell compartments, an outer ribosome-free paryphoplasm and a more central ribosome-containing pirellulosome. Some planctomycete species have three compartments, where further membranes within the pirellulosome define another compartment, the anammoxosome in anammox planctomycetes and the membrane-bounded nuclear body in Gemmata obscuriglobus. Compartments are preserved when new Cells are formed during division. Functional features which are correlated with structural Compartmentalization in planctomycetes include in G. obscuriglobus the ability to take up proteins within the paryphoplasm of the Cell by a mechanism similar to receptor-mediated endocytosis of eukaryotes. Novel molecular and Cell biology features for bacteria can be predicted to accompany such structural and functional complexity and are discussed here.
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the Cell cycle of the planctomycete gemmata obscuriglobus with respect to Cell Compartmentalization
BMC Cell Biology, 2009Co-Authors: Richard I Webb, John A FuerstAbstract:Gemmata obscuriglobus is a distinctive member of the divergent phylum Planctomycetes, all known members of which are peptidoglycan-less bacteria with a shared compartmentalized Cell structure and divide by a budding process. G. obscuriglobus in addition shares the unique feature that its nucleoid DNA is surrounded by an envelope consisting of two membranes forming an analogous structure to the membrane-bounded nucleoid of eukaryotes and therefore G. obscuriglobus forms a special model for Cell biology. Draft genome data for G. obscuriglobus as well as complete genome sequences available so far for other planctomycetes indicate that the key bacterial Cell division protein FtsZ is not present in these planctomycetes, so the Cell division process in planctomycetes is of special comparative interest. The membrane-bounded nature of the nucleoid in G. obscuriglobus also suggests that special mechanisms for the distribution of this nuclear body to the bud and for distribution of chromosomal DNA might exist during division. It was therefore of interest to examine the Cell division cycle in G. obscuriglobus and the process of nucleoid distribution and nuclear body formation during division in this planctomycete bacterium via light and electron microscopy. Using phase contrast and fluorescence light microscopy, and transmission electron microscopy, the Cell division cycle of G. obscuriglobus was determined. During the budding process, the bud was formed and developed in size from one point of the mother Cell perimeter until separation. The matured daughter Cell acted as a new mother Cell and started its own budding cycle while the mother Cell can itself initiate budding repeatedly. Fluorescence microscopy of DAPI-stained Cells of G. obscuriglobus suggested that translocation of the nucleoid and formation of the bud did not occur at the same time. Confocal laser scanning light microscopy applied to Cells stained for membranes as well as DNA confirmed the behaviour of the nucleoid and nucleoid envelope during Cell division. Electron microscopy of cryosubstituted Cells confirmed deductions from light microscopy concerning nucleoid presence in relation to the stage of budding, and showed that the nucleoid was observed to occur in both mother and bud Cells only at later budding stages. It further suggested that nucleoid envelope formed only after the nucleoid was translocated into the bud, since envelopes only appeared in more mature buds, while naked nucleoids occurred in smaller buds. Nucleoid envelope appeared to originate from the intracytoplasmic membranes (ICM) of both mother Cell and bud. There was always a connecting passage between mother Cell and bud during the budding process until separation of the two Cells. The division cycle of the nucleated planctomycete G. obscuriglobus appears to be a complex process in which chromosomal DNA is transported to the daughter Cell bud after initial formation of the bud, and this can be performed repeatedly by a single mother Cell. The division cycle of the nucleated planctomycete G. obscuriglobus is a complex process in which chromosomal nucleoid DNA is transported to the daughter Cell bud after initial formation of a bud without nucleoid. The new bud nucleoid is initially naked and not surrounded by membrane, but eventually acquires a complete nucleoid envelope consisting of two closely apposed membranes as occurs in the mother Cell. The membranes of the new nucleoid envelope surrounding the bud nucleoid are derived from intracytoplasmic membranes of both the mother Cell and the bud. The Cell division of G. obscuriglobus displays some unique features not known in Cells of either prokaryotes or eukaryotes.
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the Cell cycle of the planctomycete gemmata obscuriglobus with respect to Cell Compartmentalization
BMC Cell Biology, 2009Co-Authors: Kuochang Lee, Richard I Webb, John A FuerstAbstract:Gemmata obscuriglobus is a distinctive member of the divergent phylum Planctomycetes, all known members of which are peptidoglycan-less bacteria with a shared compartmentalized Cell structure and divide by a budding process. G. obscuriglobus in addition shares the unique feature that its nucleoid DNA is surrounded by an envelope consisting of two membranes forming an analogous structure to the membrane-bounded nucleoid of eukaryotes and therefore G. obscuriglobus forms a special model for Cell biology. Draft genome data for G. obscuriglobus as well as complete genome sequences available so far for other planctomycetes indicate that the key bacterial Cell division protein FtsZ is not present in these planctomycetes, so the Cell division process in planctomycetes is of special comparative interest. The membrane-bounded nature of the nucleoid in G. obscuriglobus also suggests that special mechanisms for the distribution of this nuclear body to the bud and for distribution of chromosomal DNA might exist during division. It was therefore of interest to examine the Cell division cycle in G. obscuriglobus and the process of nucleoid distribution and nuclear body formation during division in this planctomycete bacterium via light and electron microscopy. Using phase contrast and fluorescence light microscopy, and transmission electron microscopy, the Cell division cycle of G. obscuriglobus was determined. During the budding process, the bud was formed and developed in size from one point of the mother Cell perimeter until separation. The matured daughter Cell acted as a new mother Cell and started its own budding cycle while the mother Cell can itself initiate budding repeatedly. Fluorescence microscopy of DAPI-stained Cells of G. obscuriglobus suggested that translocation of the nucleoid and formation of the bud did not occur at the same time. Confocal laser scanning light microscopy applied to Cells stained for membranes as well as DNA confirmed the behaviour of the nucleoid and nucleoid envelope during Cell division. Electron microscopy of cryosubstituted Cells confirmed deductions from light microscopy concerning nucleoid presence in relation to the stage of budding, and showed that the nucleoid was observed to occur in both mother and bud Cells only at later budding stages. It further suggested that nucleoid envelope formed only after the nucleoid was translocated into the bud, since envelopes only appeared in more mature buds, while naked nucleoids occurred in smaller buds. Nucleoid envelope appeared to originate from the intracytoplasmic membranes (ICM) of both mother Cell and bud. There was always a connecting passage between mother Cell and bud during the budding process until separation of the two Cells. The division cycle of the nucleated planctomycete G. obscuriglobus appears to be a complex process in which chromosomal DNA is transported to the daughter Cell bud after initial formation of the bud, and this can be performed repeatedly by a single mother Cell. The division cycle of the nucleated planctomycete G. obscuriglobus is a complex process in which chromosomal nucleoid DNA is transported to the daughter Cell bud after initial formation of a bud without nucleoid. The new bud nucleoid is initially naked and not surrounded by membrane, but eventually acquires a complete nucleoid envelope consisting of two closely apposed membranes as occurs in the mother Cell. The membranes of the new nucleoid envelope surrounding the bud nucleoid are derived from intracytoplasmic membranes of both the mother Cell and the bud. The Cell division of G. obscuriglobus displays some unique features not known in Cells of either prokaryotes or eukaryotes.