bluuebunny/crossref_metadata_2025 huggingface dataset:
Transplantation of a multipotent cell population from human adipose tissue induces dystrophin expression in the immunocompetent mdx mouse
Authors: Rodriguez Anne-Marie , Pisani Didier , Dechesne Claude A. , Turc-Carel Claude , Kurzenne Jean-Yves , Wdziekonski Brigitte , Villageois Albert , Bagnis Claude , Breittmayer Jean-Philippe , Groux Hervé , Ailhaud Gérard , Dani Christian
Published: May 2005

Here, we report the isolation of a human multipotent adipose-derived stem (hMADS) cell population from adipose tissue of young donors. hMADS cells display normal karyotype; have active telomerase; proliferate >200 population doublings; and differentiate into adipocytes, osteoblasts, and myoblasts. Flow cytometry analysis indicates that hMADS cells are CD44+, CD49b+, CD105+, CD90+, CD13+, Stro-1−, CD34−, CD15−, CD117−, Flk-1−, gly-A−, CD133−, HLA-DR−, and HLA-Ilow. Transplantation of hMADS cells into the mdx mouse, an animal model of Duchenne muscular dystrophy, results in substantial expression of human dystrophin in the injected tibialis anterior and the adjacent gastrocnemius muscle. Long-term engraftment of hMADS cells takes place in nonimmunocompromised animals. Based on the small amounts of an easily available tissue source, their strong capacity for expansion ex vivo, their multipotent differentiation, and their immune-privileged behavior, our results suggest that hMADS cells will be an important tool for muscle cell–mediated therapy.
A requirement for CD45 distinguishes Ly49D-mediated cytokine and chemokine production from killing in primary natural killer cells
Authors: Huntington Nicholas D. , Xu Yuekang , Nutt Stephen L. , Tarlinton David M.
Published: May 2005

Engagement of receptors on the surface of natural killer (NK) cells initiates a biochemical cascade ultimately triggering cytokine production and cytotoxicity, although the interrelationship between these two outcomes is currently unclear. In this study we investigate the role of the cell surface phosphatase CD45 in NK cell development and intracellular signaling from activating receptors. Stimulation via the major histocompatibility complex I–binding receptor, Ly49D on CD45−/− primary NK cells resulted in the activation of phosphoinositide-3-kinase and normal cytotoxicity but failed to elicit a range of cytokines and chemokines. This blockage is associated with impaired phosphorylation of Syk, Vav1, JNK, and p38, which mimics data obtained using inhibitors of the src-family kinases (SFK). These data, supported by analogous findings after CD16 and NKG2D stimulation of CD45−/− primary NK cells, place CD45 upstream of SFK in NK cells after stimulation via immunoreceptor tyrosine-based activation motif-containing receptors. Thus we identify CD45 as a pivotal enzyme in eliciting a precise subset of NK cell responses.
Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation
Authors: Zheng Nai-Ying , Wilson Kenneth , Jared Matthew , Wilson Patrick C.
Published: May 2005

It is believed that immunoglobulin-variable region gene (IgV) somatic hypermutation (SHM) is initiated by activation-induced cytidine deaminase (AID) upon deamination of cytidine to deoxyuracil. Patch-excision repair of these lesions involving error prone DNA polymerases such as polη causes mutations at all base positions. If not repaired, the deaminated nucleotides on the coding and noncoding strands result in C-to-T and G-to-A exchanges, respectively. Herein it is reported that IgV gene evolution has been considerably influenced by the need to accommodate extensive C deaminations and the resulting accumulation of C-to-T and G-to-A exchanges. Although seemingly counterintuitive, the precise placement of C and G nucleotides causes most C-to-T and G-to-A mutations to be silent or conservative. We hypothesize that without intricate positioning of C and G nucleotides the efficiency of affinity maturation would be significantly reduced due to a dominance of replacements caused by C and G transition mutations. The complexity of these evolved biases in codon use are compounded by the precise concomitant hotspot/coldspot targeting of AID activity and Polη errors to maximize SHM in the CDRs and minimize mutations in the FWRs.
Antigenic conservation and immunogenicity of the HIV coreceptor binding site
Authors: Decker Julie M. , Bibollet-Ruche Frederic , Wei Xiping , Wang Shuyi , Levy David N. , Wang Wenquan , Delaporte Eric , Peeters Martine , Derdeyn Cynthia A. , Allen Susan , Hunter Eric , Saag Michael S. , Hoxie James A. , Hahn Beatrice H. , Kwong Peter D. , Robinson James E. , Shaw George M.
Published: May 2005

Immunogenic, broadly reactive epitopes of the HIV-1 envelope glycoprotein could serve as important targets of the adaptive humoral immune response in natural infection and, potentially, as components of an acquired immune deficiency syndrome vaccine. However, variability in exposed epitopes and a combination of highly effective envelope-cloaking strategies have made the identification of such epitopes problematic. Here, we show that the chemokine coreceptor binding site of HIV-1 from clade A, B, C, D, F, G, and H and circulating recombinant form (CRF)01, CRF02, and CRF11, elicits high titers of CD4-induced (CD4i) antibody during natural human infection and that these antibodies bind and neutralize viruses as divergent as HIV-2 in the presence of soluble CD4 (sCD4). 178 out of 189 (94%) HIV-1–infected patients had CD4i antibodies that neutralized sCD4-pretreated HIV-2 in titers (50% inhibitory concentration) as high as 1:143,000. CD4i monoclonal antibodies elicited by HIV-1 infection also neutralized HIV-2 pretreated with sCD4, and polyclonal antibodies from HIV-1–infected humans competed specifically with such monoclonal antibodies for binding. In vivo, variants of HIV-1 with spontaneously exposed coreceptor binding surfaces were detected in human plasma; these viruses were neutralized directly by CD4i antibodies. Despite remarkable evolutionary diversity among primate lentiviruses, functional constraints on receptor binding create opportunities for broad humoral immune recognition, which in turn serves to constrain the viral quasispecies.
Sustained expansion of NKT cells and antigen-specific T cells after injection of α-galactosyl-ceramide loaded mature dendritic cells in cancer patients
Authors: Chang David H. , Osman Keren , Connolly John , Kukreja Anjli , Krasovsky Joseph , Pack Maggi , Hutchinson Aisha , Geller Matthew , Liu Nancy , Annable Rebecca , Shay Jennifer , Kirchhoff Kelly , Nishi Nobusuke , Ando Yoshitaka , Hayashi Kunihiko , Hassoun Hani , Steinman Ralph M. , Dhodapkar Madhav V.
Published: May 2005

Natural killer T (NKT) cells are distinct glycolipid reactive innate lymphocytes that are implicated in the resistance to pathogens and tumors. Earlier attempts to mobilize NKT cells, specifically, in vivo in humans met with limited success. Here, we evaluated intravenous injection of monocyte-derived mature DCs that were loaded with a synthetic NKT cell ligand, α-galactosyl-ceramide (α-GalCer; KRN-7000) in five patients who had advanced cancer. Injection of α-GalCer–pulsed, but not unpulsed, dendritic cells (DCs) led to >100-fold expansion of several subsets of NKT cells in all patients; these could be detected for up to 6 mo after vaccination. NKT activation was associated with an increase in serum levels of interleukin-12 p40 and IFN-γ inducible protein-10. In addition, there was an increase in memory CD8+ T cells specific for cytomegalovirus in vivo in response to α-GalCer–loaded DCs, but not unpulsed DCs. These data demonstrate the feasibility of sustained expansion of NKT cells in vivo in humans, including patients who have advanced cancer, and suggest that NKT activation might help to boost adaptive T cell immunity in vivo.
PU.1 regulates the commitment of adult hematopoietic progenitors and restricts granulopoiesis
Authors: Dakic Aleksandar , Metcalf Donald , Di Rago Ladina , Mifsud Sandra , Wu Li , Nutt Stephen L.
Published: May 2005

Although the transcription factor PU.1 is essential for fetal lymphomyelopoiesis, we unexpectedly found that elimination of the gene in adult mice allowed disturbed hematopoiesis, dominated by granulocyte production. Impaired production of lymphocytes was evident in PU.1-deficient bone marrow (BM), but myelocytes and clonogenic granulocytic progenitors that are responsive to granulocyte colony-stimulating factor or interleukin-3 increased dramatically. No identifiable common lymphoid or myeloid progenitor populations were discernable by flow cytometry; however, clonogenic assays suggested an overall increased frequency of blast colony-forming cells and BM chimeras revealed existence of long-term self-renewing PU.1-deficient cells that required PU.1 for lymphoid, but not granulocyte, generation. PU.1 deletion in granulocyte-macrophage progenitors, but not in common myeloid progenitors, resulted in excess granulocyte production; this suggested specific roles of PU.1 at different stages of myeloid development. These findings emphasize the distinct nature of adult hematopoiesis and reveal that PU.1 regulates the specification of the multipotent lymphoid and myeloid compartments and restrains, rather than promotes, granulopoiesis.
Blocking IL-1 in systemic inflammation
Authors: Dinarello Charles A.
Published: May 2005

A growing number of systemic inflammatory diseases characterized in part by recurrent fevers, leukocytosis, anemia, and elevated acute phase proteins are linked to interleukin (IL)-1 activity since rapid and sustained resolution is observed upon specific blockade of IL-1 receptors. Rapid resolution of systemic and local inflammation is now also reported in systemic onset juvenile idiopathic arthritis (SoJIA). Loss of control of the secretion of IL-1β might be a common mechanism explaining the aberrant activity of IL-1 in these diseases.
Harry Goldblatt and the discovery of renin
Authors: Van Epps Heather L.
Published: May 2005

In 1934, pathologist Harry Goldblatt established the first animal model of hypertension. This model provided researchers with the tools to delineate the renin-angiotensin system of blood pressure control and, eventually, to design enzyme inhibitors for the treatment of chronic hypertension.
Calcium-induced Human Keratinocyte Differentiation Requiressrc- andfyn-mediated Phosphatidylinositol 3-Kinase–dependent Activation of Phospholipase C-γ1
Authors: Xie Zhongjian , Singleton Patrick A. , Bourguignon Lilly Y.W. , Bikle Daniel D.
Published: May 2005

We have previously demonstrated that phospholipase C (PLC)-γ1 is required for calcium-induced human keratinocyte differentiation. In the present study, we investigated whether the activation of PLC-γ1 by nonreceptor kinases such as src and fyn plays a role in mediating this process. Our results showed that the combination of dominant negative src and fyn blocked calcium-stimulated PLC-γ1 activity and human keratinocyte differentiation, whereas each separately has little effect. However, unlike the activation of PLC-γ1 by epidermal growth factor, calcium-induced activation of PLC-γ1 was not a result of direct tyrosine phosphorylation. Therefore, we examined an alternative mechanism, in particular phosphatidylinositol 3,4,5-triphosphate (PIP3) formed as a product of phosphatidylinositol 3-kinase (PI3K) activity. PIP3binds to and activates PLC-γ1. The combination of dominant negative src and fyn blocked calcium-induced tyrosine phosphorylation of the regulatory subunit of PI3K, p85α, and the activity of the catalytic subunit of PI3K. PI3K inhibitors blocked calcium activation of PLC-γ1 as well as the induction of keratinocyte differentiation markers involucrin and transglutaminase. These data indicate that calcium activates PLC-γ1 via increased PIP3formation mediated by c-src– and fyn-activated PI3K. This activation is required for calcium-induced human keratinocyte differentiation.
“The Right Man”: James A. Jackson and the Origins of U.S. Government Interest in Black Business
Authors: Weems Robert E. , Randolph Lewis A.
Published: May 2005

Despite the widely held notion that U.S. government assistance to African American entrepreneurs commenced in the late 1960s, the evidence indicates that government interest in promoting black business actually began in the 1920s. Beginning with the appointment of James A. Jackson in November 1927, the U.S. Commerce Department’s agenda, until the mid-1950s, included “Negro Affairs.” Jackson’s actions did not generate the direct financial assistance to black entrepreneurs associated with such later government initiatives as Richard Nixon’s “Black Capitalism.” Nevertheless, Jackson’s pioneering efforts, to provide black businesspeople with useful information, helped to positively reshape contemporary African American entrepreneurs’ beliefs about the role of government in their lives.
The dynamics of visual adaptation to faces
Authors: Leopold David A , Rhodes Gillian , Müller Kai-Markus , Jeffery Linda
Published: May 2005

Several recent demonstrations using visual adaptation have revealed high-level aftereffects for complex patterns including faces. While traditional aftereffects involve perceptual distortion of simple attributes such as orientation or colour that are processed early in the visual cortical hierarchy, face adaptation affects perceived identity and expression, which are thought to be products of higher-order processing. And, unlike most simple aftereffects, those involving faces are robust to changes in scale, position and orientation between the adapting and test stimuli. These differences raise the question of how closely related face aftereffects are to traditional ones. Little is known about the build-up and decay of the face aftereffect, and the similarity of these dynamic processes to traditional aftereffects might provide insight into this relationship. We examined the effect of varying the duration of both the adapting and test stimuli on the magnitude of perceived distortions in face identity. We found that, just as with traditional aftereffects, the identity aftereffect grew logarithmically stronger as a function of adaptation time and exponentially weaker as a function of test duration. Even the subtle aspects of these dynamics, such as the power-law relationship between the adapting and test durations, closely resembled that of other aftereffects. These results were obtained with two different sets of face stimuli that differed greatly in their low-level properties. We postulate that the mechanisms governing these shared dynamics may be dissociable from the responses of feature-selective neurons in the early visual cortex.
Asticcacaulis taihuensis sp. nov., a novel stalked bacterium isolated from Taihu Lake, China
Authors: Liu Zhi-Pei , Wang Bao-Jun , Liu Shuang-Jiang , Liu Ying-Hao
Published: May 2005

A novel stalked bacterium, designated strain T3-B7T, was isolated from sediment of Taihu Lake, Jiangsu Province, China, and its taxonomy was studied by using a polyphasic approach. Cell morphology, physiological and biochemical properties, and polar lipids indicated that strain T3-B7T represented a member of the genus Asticcacaulis. Based on 16S rRNA gene sequence similarity analysis, strain T3-B7T was found to be phylogenetically related to Asticcacaulis biprosthecium DSM 4723T (98·5 %) and Asticcacaulis excentricus DSM 4724T (95·0 %), but could be differentiated from these two species on the basis of the number and position of prosthecae, assimilation of sugars, nitrate reduction and tolerance to NaCl. Levels of DNA–DNA relatedness of strain T3-B7T to A. biprosthecium DSM 4723T and A. excentricus DSM 4724T were 37·1 and 18·0 %, respectively. The G+C content of strain T3-B7T was 59 mol% (T
m). It is concluded that strain T3-B7T represents a novel species of the genus Asticcacaulis, for which the name of Asticcacaulis taihuensis sp. nov. is proposed. The type strain is T3-B7T (=AS 1.3431T=JCM 12463T).
Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis)
Authors: Rhodes Martha W. , Kator Howard , McNabb Alan , Deshayes Caroline , Reyrat Jean-Marc , Brown-Elliott Barbara A. , Wallace Richard , Trott Kristin A. , Parker John M. , Lifland Barry , Osterhout Gerard , Kaattari Ilsa , Reece Kimberly , Vogelbein Wolfgang , Ottinger Christopher A.
Published: May 2005

A group of slowly growing photochromogenic mycobacteria was isolated from Chesapeake Bay striped bass (Morone saxatilis) during an epizootic of mycobacteriosis. Growth characteristics, acid-fastness and 16S rRNA gene sequencing results were consistent with those of the genus Mycobacterium. Biochemical reactions, growth characteristics and mycolic acid profiles (HPLC) resembled those of Mycobacterium shottsii, a non-pigmented mycobacterium also isolated during the same epizootic. Sequencing of the 16S rRNA genes, the gene encoding the exported repeated protein (erp) and the gene encoding the 65 kDa heat-shock protein (hsp65) and restriction enzyme analysis of the hsp65 gene demonstrated that this group of isolates is unique. Insertion sequences associated with Mycobacterium ulcerans, IS2404 and IS2606, were detected by PCR. These isolates could be differentiated from other slowly growing pigmented mycobacteria by their inability to grow at 37 °C, production of niacin and urease, absence of nitrate reductase, negative Tween 80 hydrolysis and resistance to isoniazid (1 μg ml−1), p-nitrobenzoic acid, thiacetazone and thiophene-2-carboxylic hydrazide. On the basis of this polyphasic study, it is proposed that these isolates represent a novel species, Mycobacterium pseudoshottsii sp. nov. The type strain, L15T, has been deposited in the American Type Culture Collection as ATCC BAA-883T and the National Collection of Type Cultures (UK) as NCTC 13318T.
Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus
Authors: Perevalova A. A. , Svetlichny V. A. , Kublanov I. V. , Chernyh N. A. , Kostrikina N. A. , Tourova T. P. , Kuznetsov B. B. , Bonch-Osmolovskaya E. A.
Published: May 2005

An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain Z-1312T, was isolated from a freshwater hot spring of the Uzon caldera (Kamchatka Peninsula, Russia). The cells were regular cocci, 1–4 μm in diameter, with one long flagellum. The cell envelope was composed of a globular layer attached to the cytoplasmic membrane. The temperature range for growth was 63–89 °C, with an optimum between 80 and 82 °C. The pH range for growth at 80 °C was 4·8–6·8, with an optimum at pH 6·0. Strain Z-1312Tgrew by hydrolysis and/or fermentation of a wide range of polymeric and monomeric substrates, including agarose, amygdalin, arabinose, arbutin, casein hydrolysate, cellulose (filter paper, microcrystalline cellulose, carboxymethyl cellulose), dextran, dulcitol, fructose, lactose, laminarin, lichenan, maltose, pectin, peptone, ribose, starch and sucrose. No growth was detected on glucose, xylose, mannitol or sorbitol. Growth products when sucrose or starch were used as the substrate were acetate, H2and CO2. Elemental sulfur, thiosulfate and nitrate added as potential electron acceptors for anaerobic respiration did not stimulate growth when tested with starch as the substrate. H2at 100 % in the gas phase did not inhibit growth on starch or peptone. The G+C content of the DNA was 42·5 mol%. 16S rRNA gene sequence analysis placed the isolated strain Z-1312Tas a member of the genusDesulfurococcus, where it represented a novel species, for which the nameDesulfurococcus fermentanssp. nov. (type strain Z-1312T=DSM 16532T=VKM V-2316T) is proposed.
Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil
Authors: Zhang Yu-Qin , Li Wen-Jun , Kroppenstedt Reiner M. , Kim Chang-Jin , Chen Guo-Zhong , Park Dong-Jin , Xu Li-Hua , Jiang Cheng-Lin
Published: May 2005

A Gram-positive, aerobic, non-motile, mesophilic strain, designated YIM 70056T, was isolated from a forest soil sample in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had less than 97·0 % similarity to anyRhodococcusspecies with validly published names, with the exception ofRhodococcus fascians(DSM 20669T), which was found to be its closest neighbour (98·9 % similarity). Chemotaxonomic data, including peptidoglycan type, diagnostic sugar compositions, fatty acid profiles, menaquinones, polar lipids and mycolic acids, were determined for this isolate; the results supported the affiliation of strain YIM 70056Tto the genusRhodococcus. The DNA G+C content was 63·5 mol%. The results of DNA–DNA hybridization withR. fasciansDSM 20669T, in combination with chemotaxonomic and physiological data, demonstrated that isolate YIM 70056Trepresents a novelRhodococcusspecies, for which the nameRhodococcus yunnanensissp. nov. is proposed, with YIM 70056T(=CCTCC AA 204007T=KCTC 19021T=DSM 44837T) as the type strain.
Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov., two novel thermoacidophiles isolated from geothermal soils of northern Victoria Land, Antarctica
Authors: Allan R. N. , Lebbe L. , Heyrman J. , De Vos P. , Buchanan C. J. , Logan N. A.
Published: May 2005

Thirteen strains of endospore-forming bacteria were isolated from geothermal soils at Cryptogam Ridge, the north-west slope of Mt Melbourne, and at the vents and summit of Mt Rittmann in northern Victoria Land, Antarctica. 16S rRNA gene sequencing, SDS-PAGE and routine phenotypic characterization tests indicated that the seven isolates from the north-west slope of Mt Melbourne represent a novel species ofBrevibacillusand that the six isolates from Cryptogam Ridge and the vents and summit of Mt Rittmann represent a novel species ofAneurinibacillus.Brevibacillusstrains were not isolated from the sites at Mt Rittmann or Cryptogam Ridge andAneurinibacillusstrains were not isolated from the north-west slope of Mt Melbourne. Preliminary metabolic studies revealed thatl-glutamic acid, although not essential for growth, was utilized by both species. TheBrevibacillusspecies possessed an uptake system specific forl-glutamic acid, whereas theAneurinibacillusspecies possessed a more general uptake system capable of transporting other related amino acids. Both species utilized a K+antiport system and similar energy systems for the uptake ofl-glutamic acid. The rate of uptake by theBrevibacillusspecies type strain was 20-fold greater than that shown by theAneurinibacillusspecies type strain. The namesBrevibacillus levickiisp. nov. andAneurinibacillus terranovensissp. nov. are proposed for the novel taxa; the type strains are Logan B-1657T(=LMG 22481T=CIP 108307T) and Logan B-1599T(LMG 22483T=CIP 108308T), respectively.
Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa
Authors: Xie Cheng-Hui , Yokota Akira
Published: May 2005

Five strains of free-living diazotrophs isolated from rice were characterized by using a polyphasic approach. The strains were found to be very closely related, with 99–100 % 16S rRNA gene sequence similarity and DNA–DNA hybridization values greater than 70 %, suggesting that they represent a single species. When compared with other recognized species, they showed not more than 93 and 89 % similarity for the 16S rRNA and nifH gene sequences, respectively. Phylogenetic distances showed that these isolates were distinct from other taxa within the α-Proteobacteria. Chemotaxonomic characteristics of these isolates included the DNA G+C content (62·1–63·1 mol%), the major quinone system (Q-10), predominant fatty acids (18 : 1ω7c, cyclo 19 : 0ω8c and 16 : 0) and major hydroxy fatty acids (14 : 0 3-OH, 18 : 0 3-OH and 16 : 0 3-OH). Based on phylogenetic and phenotypic analyses, these isolates are considered to represent a novel genus and species, for which the name Pleomorphomonas oryzae gen. nov., sp. nov. is proposed. The type strain is F-7T (=IAM 15079T=ATCC BAA-940T=DSM 16300T).
Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China
Authors: Xu Ping , Li Wen-Jun , Tang Shu-Kun , Zhang Yu-Qin , Chen Guo-Zhong , Chen Hua-Hong , Xu Li-Hua , Jiang Cheng-Lin
Published: May 2005

A taxonomic study was performed on strain YIM 31775T, which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 °C and 6·5 to 12·0, respectively; the optimum growth temperature and pH were 28–37 °C and 7·0–9·0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C16 : 1
ω7c (42·4 %) and C16 : 0 (28·1 %). The DNA G+C content was 62·4±0·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775T should be placed within the family ‘Oxalobacteraceae’, in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775T should be classified as representing a novel member of the family ‘Oxalobacteraceae’, for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775T (=CCTCC AA 204003T=KCTC 12194T).
Reclassification of [Cytophaga] marinoflava Reichenbach 1989 as Leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of Leeuwenhoekiella aequorea sp. nov.
Authors: Nedashkovskaya Olga I. , Vancanneyt Marc , Dawyndt P. , Engelbeen Katrien , Vandemeulebroecke Katrien , Cleenwerck Ilse , Hoste Bart , Mergaert Joris , Tan Tjhing-Lok , Frolova Galina M. , Mikhailov Valery V. , Swings Jean
Published: May 2005

Five heterotrophic, aerobic, halotolerant and pigmented bacterial strains with gliding motility were isolated from Antarctic sea water; one other isolate was collected from the sea urchinStrongylocentrotus intermediusin the Gulf of Peter the Great in the Sea of Japan. 16S rRNA gene sequence analysis indicated that the strains are members of the familyFlavobacteriaceae, the nearest neighbour (with 97·1 % sequence similarity) being the misclassified species [Cytophaga]marinoflava. DNA–DNA hybridization experiments and chemotaxonomic and phenotypic analyses demonstrated that the six novel isolates represent a single species distinct from [C.]marinoflava. On the basis of its separate phylogenetic lineage (the nearest neighbours show 92 % sequence similarity), [C.]marinoflavais reclassified asLeeuwenhoekiella marinoflavagen. nov., comb. nov. A second species of this new genus,Leeuwenhoekiella aequoreasp. nov., is proposed for the six novel isolates, with strain LMG 22550T(=CCUG 50091T) as the type strain.
Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough
Authors: Bae Seung Seob , Lee Jung-Hyun , Kim Sang-Jin
Published: May 2005

Two thermophilic, spore-forming strains, TM1Tand TM5, were isolated from deep-sea sediment (4000 m below sea level) of the Ayu Trough in the western Pacific Ocean. Cells of the two strains were Gram-positive, motile and rod-shaped. Their spores were ellipsoidal, subterminal to terminal and occurred in swollen sporangia. The two strains grew at temperatures up to 65 °C and in the pH range 6·5–9·0. The NaCl concentration for optimal growth was 3·0 % (w/v) and growth was inhibited by 5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains TM1Tand TM5 belonged to the genusBacillus, and that strain TM1Twas most closely related toBacillus aeoliusDSM 15084T(96·7 %),Bacillus smithiiDSM 4216T(96·1 %),Bacillus methanolicusNCIMB 13113T(95·8 %) andBacillus pallidusDSM 3670T(95·7 %). Between the 16S rRNA gene sequences of strains TM1Tand TM5 there were only three nucleotide differences, implying that the two strains were of the same species. The cellular fatty acid profiles of the two strains were also very similar, with iso-C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0and anteiso-C17 : 0as the major components. The G+C content of strain TM1Twas 38·7 %. On the basis of phenotypic and molecular data, strains TM1Tand TM5 represent a novel species of the genusBacillus, for which the nameBacillus alveayuensissp. nov. is proposed. The type strain is TM1T(=KCTC 10634T=JCM 12523T).
Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus
Authors: Zeigler Daniel R.
Published: May 2005

Full-lengthrecNand 16S rRNA gene sequences were determined for a collection of 68 strains from the thermophilic Gram-positive genusGeobacillus, members of which have been isolated from geographically and ecologically diverse locations. Phylogenetic treeing methods clustered the isolates into nine sequence similarity groups, regardless of which gene was used for analysis. Several of these groups corresponded unambiguously to knownGeobacillusspecies, whereas others contained two or more type strains from species with validly published names, highlighting a need for a re-assessment of the taxonomy for this genus. For taxonomic analysis of bacteria related at a genus, species or subspecies level,recNsequence comparisons had a resolving power nearly an order or magnitude greater than 16S rRNA gene comparisons. Mutational saturation renderedrecNcomparisons much less powerful than 16S rRNA gene comparisons for analysis of higher taxa, however. Analysis ofrecNsequences should prove a powerful tool for assigning strains to species withinGeobacillus, and perhaps within other genera as well.
Streptomyces sodiiphilus sp. nov., a novel alkaliphilic actinomycete
Authors: Li Wen-Jun , Zhang Yong-Guang , Zhang Yu-Qin , Tang Shu-Kun , Xu Ping , Xu Li-Hua , Jiang Cheng-Lin
Published: May 2005

An alkaliphilic actinomycete, strain YIM 80305T, which was isolated from a muddy sample in Chaka salt lake, Qinghai Province of China, was characterized using a polyphasic approach. The isolate produced light-yellow substrate and yellow–white aerial mycelia on most tested media. Optimum pH for growth was 9·0–10·0 with scant growth at pH 7·0. Results showed that strain YIM 80305T was obligately Na+-dependent, and showed sensitivity to K+. The DNA G+C content was 70·5 mol%. 16S rRNA gene sequence analysis together with these characteristics consistently assigned strain YIM 80305T to the genus Streptomyces. It formed a distinct clade based on analyses of the almost-complete and 120-nucleotide variable γ region of the 16S rRNA gene. It could be differentiated by phenotypic and genotypic analysis from all the Streptomyces species whose names have been validly published. On the basis of polyphasic evidence, Streptomyces sodiiphilus sp. nov. is proposed. The type strain is YIM 80305T (=CCTCC AA 203015T=CIP 107975T).
Lentibacillus salarius sp. nov., isolated from saline sediment in China, and emended description of the genus Lentibacillus
Authors: Jeon Che Ok , Lim Jee-Min , Lee Jae-Chan , Lee Gye Suk , Lee Jung-Min , Xu Li-Hua , Jiang Cheng-Lin , Kim Chang-Jin
Published: May 2005

A Gram-positive, spore-forming and moderately halophilic bacterium, strain BH139T, was isolated from saline sediment of Xinjiang Province, China. Cells of strain BH139Twere motile, flagellated rods. The organism grew optimally at 30–35 °C in the presence 12–14 % (w/v) NaCl. The major fatty acids were branched saturated fatty acids such as iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0and anteiso-C17 : 0. The G+C content of the genomic DNA was about 43 mol% and the predominant isoprenoid quinone was MK-7. Comparative 16S rRNA gene sequence analyses showed that strain BH139Twas most closely related toLentibacillus salicampiKCCM 41560T(96·9 % 16S rRNA gene sequence similarity) and formed a distinct phyletic line from that species. On the basis of physiological and molecular properties, the isolate represents a novel species within the genusLentibacillus, for which the nameLentibacillus salariussp. nov. is proposed. The type strain is BH139T(=KCTC 3911T=DSM 16459T).
Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm
Authors: Ito Tsukasa , Sugita Kenichi , Yumoto Isao , Nodasaka Yoshinobu , Okabe Satoshi
Published: May 2005

A novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain SO07T, was isolated from a microaerobic waste-water biofilm. Chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Anaerobic and heterotrophic growth were not observed. Nitrate was not used as a terminal electron acceptor. The optimum pH and temperature for growth were pH 7·5 and 30 °C, respectively. The major isoprenoid quinone was Q-8. The DNA G+C content of strain SO07T was 47·1 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain SO07T formed a monophyletic group in the γ-Proteobacteria with only 89 % similarity to members of the genus Halothiobacillus, its nearest phylogenetic neighbours. In addition, the isolate differed from members of the genus Halothiobacillus in its requirement for and tolerance of NaCl; strain SO07T was unable to grow in NaCl concentrations of more than 180 mM. On the basis of phylogenetic, chemotaxonomic and physiological data, it is proposed that isolate SO07T (=JCM 12417T=ATCC BAA-1033T) represents the type strain of a novel species in a new genus, Thiovirga sulfuroxydans gen. nov., sp. nov.
Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China
Authors: Liu Zhi-Pei , Wang Bao-Jun , Liu Ying-Hao , Liu Shuang-Jiang
Published: May 2005

A novel aromatic-compound-degrading bacterium, strain T3-B9T, was isolated from sediment of Taihu Lake, Jiangsu Province, south-east China. This bacterial isolate assimilated several aromatic compounds such as phenol, aniline, nitrobenzene, 4-chloronitrobenzene and phenanthrene. The taxonomy of strain T3-B9Twas studied by polyphasic methods. The organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genusNovosphingobium. The 16S rRNA gene sequence similarity of strain T3-B9Tto members of the genusNovosphingobiumranged from 91·6 to 97·5 %, and this isolate clustered phylogenetically with members of genusNovosphingobium. The DNA–DNA relatedness values of strain T3-B9Tto the most phylogenetically related species,Novosphingobium subterraneumDSM 12447T,Novosphingobium aromaticivoransATCC 700278TandNovosphingobium stygiumATCC 700280T, were 31, 33 and 14 %, respectively. The combined genotypic and phenotypic data show that strain T3-B9Trepresents a novel species of the genusNovosphingobium, for which the nameNovosphingobium taihuensesp. nov. is proposed. The type strain is T3-B9T(=AS 1.3432T=JCM 12465T).
Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents
Authors: Robertson Bronwyn R. , O'Rourke Jani L. , Neilan Brett A. , Vandamme Peter , On Stephen L. W. , Fox James G. , Lee Adrian
Published: May 2005

The mammalian gastrointestinal tract is covered by a layer of mucus that can harbour a range of bacterial species specifically adapted to colonize this ecological niche. Examination of 110 bacterial isolates cultivated from the gastrointestinal tract of 23 mice revealed the presence of a subgroup of 30 isolates that did not correspond genetically with genera commonly associated with this site, i.e. members of the ε-Proteobacteria such as Helicobacter and Campylobacter species. Instead this group of isolates was found to lie within the phylum Deferribacteres, a completely distinct lineage in the domain Bacteria. There was a high level of consensus in results obtained from the phenotypic and genotypic characterization of a number of the isolates, which showed they were distinct from other members of the Deferribacteres. As such, they are proposed to constitute a new genus and species, Mucispirillum schaedleri gen. nov., sp. nov. These organisms are anaerobic, Gram-negative, spiral-shaped rods with bipolar flagella. The type strain is HRI I17T (=ATCC BAA-1009T=ACM 5223T).
Bacillus arsenicus sp. nov., an arsenic-resistant bacterium isolated from a siderite concretion in West Bengal, India
Authors: Shivaji S. , Suresh K. , Chaturvedi Preeti , Dube Smita , Sengupta S.
Published: May 2005

Strain Con a/3Tis a Gram-positive, motile, endospore-forming, rod-shaped and arsenic-resistant bacterium, which was isolated from a concretion of arsenic ore obtained from a bore-hole. The bacterium grew in the presence of 20 mM arsenate and 0·5 mM arsenite. Diaminopimelic acid was present in the cell wall peptidoglycan, MK-7 was the major menaquinone, and iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0and C16 : 1(δ7cis) were the major fatty acids. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain Con a/3Twas identified as a member of the genusBacillus. It exhibited maximum similarity (97 %) at the 16S rRNA gene level withBacillus barbaricus(DSM 14730T); however, the DNA–DNA relatedness value withB. barbaricuswas 60 %. Strain Con a/3Talso exhibited a number of phenotypic differences fromB. barbaricus(DSM 14730T). Strain Con a/3Twas therefore identified as representing a novel species of the genusBacillus, for which the nameBacillus arsenicussp. nov. is proposed. The type strain is Con a/3T(=MTCC 4380T=DSM 15822T=JCM 12167T).
Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa
Authors: Horn Marcus A. , Ihssen Julian , Matthies Carola , Schramm Andreas , Acker Georg , Drake Harold L.
Published: May 2005

Earthworms emit nitrous oxide (N2O) via the activity of bacteria in their gut. Four N2O-producing facultative aerobes, ED1T, ED5T, MH21T and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N2O under conditions that simulated the microenvironment of the earthworm gut. ED1T and ED5T were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N2) and contained membranous c-type cytochromes. ED1T grew optimally at 30 °C and pH 7. ED1T oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1T was Dechloromonas agitata. ED5T grew optimally at 25 °C and pH 7. ED5T grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5T were Flavobacterium johnsoniae and Flavobacterium flevense. MH21T and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21T and MH72. Cells of MH21T grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21T grew optimally at 30–35 °C and pH 7·7, grew by fermentation and reduced low amounts of nitrite to N2O. The closest phylogenetic relatives of MH21T were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1T (=DSM 15892T=ATCC BAA-841T), ED5T (=DSM 15936T=ATCC BAA-842T) and MH21T (=DSM 15890T=ATCC BAA-844T) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.
Mycobacterium florentinum sp. nov., isolated from humans
Authors: Tortoli Enrico , Rindi Laura , Goh Khye S. , Katila Marja L. , Mariottini Alessandro , Mattei Romano , Mazzarelli Gianna , Suomalainen Sini , Torkko Pirjo , Rastogi Nalin
Published: May 2005

Eight mycobacterial strains isolated during an 11 year period from the sputum of independent patients with various pulmonary disorders and, in one case, from a lymph node of a young girl, were found to present identical features. Phenotypic and genotypic characteristics revealed that the most closely related species to these test isolates wereMycobacterium triplexandMycobacterium lentiflavum. However, the lipids of the cell wall of the test isolates differed from those of the latter species by TLC and presented unique profiles by both GC and HPLC. Genotypic analysis showed that they had unique 16S rRNA gene and internal transcribed spacer (ITS) sequences, and could be differentiated from all other mycobacterial strains by PCR restriction analysis ofhsp65. The strains presented high resistance to antimycobacterial drugs. The nameMycobacterium florentinumsp. nov. is proposed for this taxon, with strain FI-93171T(=DSM 44852T=CIP 108409T) as the type strain.
Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus
Authors: Lim Jee-Min , Jeon Che Ok , Park Dong-Jin , Kim Hye-Ryoung , Yoon Byoung-Jun , Kim Chang-Jin
Published: May 2005

A moderately halophilic, Gram-positive, rod-shaped bacterium (BH030004T) was isolated from a solar saltern in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BH030004Tbelonged to the genusPontibacillus. Chemotaxonomic data (DNA G+C content, 42 mol%; major isoprenoid quinone, MK-7; cell-wall type, A1γ-typemeso-diaminopimelic acid; major fatty acids, iso-C15 : 0and anteiso-C15 : 0) also supported the affiliation of the isolate to the genusPontibacillus. Although the 16S rRNA gene sequence similarity between strain BH030004TandPontibacillus chungwhensisDSM 16287Twas relatively high (99·1 %), physiological properties and DNA–DNA hybridization (about 7 % DNA–DNA relatedness) allowed genotypic and phenotypic differentiation of strain BH030004Tfrom the type strain ofP. chungwhensis. Therefore, strain BH030004Trepresents a novel species of the genusPontibacillus, for which the namePontibacillus marinussp. nov. is proposed. The type strain is BH030004T(=KCTC 3917T=DSM 16465T).
Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Lee Choong-Hwan , Yeo Soo-Hwan , Oh Tae-Kwang
Published: May 2005

A Gram-negative, motile, slightly halophilic bacterial strain, SW-150T, was isolated from sea water of the Yellow Sea, Korea, and was characterized by a polyphasic taxonomic approach. Strain SW-150Tgrew optimally at 25–30 °C and in the presence of 2 % (w/v) NaCl. The isolate could be distinguished from otherSphingopyxisspecies in producing an orange pigment. It contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1ω7cand C17 : 1ω6cas the major fatty acids. No 3-hydroxy fatty acids were detected. Major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SW-150Twas phylogenetically affiliated to the genusSphingopyxisof the familySphingomonadaceae. Similarity values between the 16S rRNA gene sequences of strain SW-150Tand the type strains ofSphingopyxisspecies ranged from 91·6 to 94·2 %, making it possible to categorize strain SW-150Tas a species that is separate from previously describedSphingopyxisspecies. On the basis of phenotypic properties and phylogenetic distinctiveness, SW-150T(=KCTC 12231T=DSM 16222T) should be classified as the type strain of a novelSphingopyxisspecies, for which the nameSphingopyxis baekryungensissp. nov. is proposed.
Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders ‘Rhodobacterales’ and Caulobacterales
Authors: Badger Jonathan H. , Eisen Jonathan A. , Ward Naomi L.
Published: May 2005

Hyphomonas neptunium is a marine prosthecate α-proteobacterium currently classified as a member of the order ‘Rhodobacterales’. Although this classification is supported by 16S rRNA gene sequence phylogeny, 23S rRNA gene sequence analysis, concatenated ribosomal proteins, HSP70 and EF-Tu phylogenies all support classifying Hyphomonas neptunium as a member of the Caulobacterales instead. The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed.
Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates
Authors: Biebl Hanno , Allgaier Martin , Tindall Brian J. , Koblizek Michal , Lünsdorf Heinrich , Pukall Rüdiger , Wagner-Döbler Irene
Published: May 2005

A novel group of aerobic anoxygenic phototrophic bacteria was isolated from marine dinoflagellates, and two strains were characterized in detail. Cells were Gram-negative cocci or ovoid rods and were motile by means of a single, polarly inserted flagellum. They were obligate aerobes requiring 1–7 % salinity. The optimal pH range for growth was 6·5–9·0 and the temperature optimum was 33 °C. The bacteria contained bacteriochlorophyll a and spheroidenone as the only carotenoid. The in vivo absorption spectrum displayed two maxima in the infrared region at 804 and 868 nm. The distinct 804 nm band indicates the presence of light-harvesting system 2. Various organic carbon sources were assimilated, including many carboxylic acids, glucose and glycerol, but not butyrate, ethanol or methanol. Dissimilatory nitrate reduction was found for both strains. The physiological characteristics of the new strains resembled those of Roseobacter denitrificans, but there were differences in the lipid composition. Based on 16S rRNA gene sequence analysis the new strains are relatively distant from other recognized species, with the closest relatives Jannaschia helgolandensis, Ruegeria atlantica and Rhodobacter veldkampii showing 94·1–93·4 % similarity. Similarity to Roseobacter denitrificans was only 92·2 %, in line with numerous other species of the Roseobacter group. Therefore, it is proposed to classify the strains in a new genus and species within the Roseobacter clade, Dinoroseobacter shibae gen. nov., sp. nov. The type strain is DFL 12T (=DSM 16493T=NCIMB 14021T).
Paenibacillus rhizosphaerae sp. nov., isolated from the rhizosphere of Cicer arietinum
Authors: Rivas Raúl , Gutiérrez Carmen , Abril Adriana , Mateos Pedro F. , Martínez-Molina Eustoquio , Ventosa Antonio , Velázquez Encarna
Published: May 2005

Two sporulating bacterial strains designated CECAP06Tand CECAP16 were isolated from the rhizosphere of the legumeCicer arietinumin Argentina. Almost-complete 16S rRNA gene sequences identified the isolates as aPaenibacillusspecies. It was most closely related toPaenibacillus cinerisLMG 18439T(99·6 % sequence similarity),Paenibacillus favisporusLMG 20987T(99·4 % sequence similarity) andPaenibacillus azoreducensDSM 13822T(97·7 % sequence similarity). The cells of this novel species were motile, sporulating, rod-shaped, Gram-positive and strictly aerobic. The predominant fatty acids were anteiso-C15 : 0, C16 : 0and iso-C16 : 0. The DNA G+C content of strains CECAP06Tand CECAP16 was 51·3 and 50·9 mol%, respectively. Growth was observed from many carbohydrates, but gas production was not observed from glucose. Catalase and oxidase activities were present. The isolates producedβ-galactosidase and hydrolysed aesculin. Gelatinase, caseinase and urease were not produced. The results of DNA–DNA hybridization showed that the strains from this study constitute a novel species of the genusPaenibacillus, for which the namePaenibacillus rhizosphaeraesp. nov. is proposed. The type strain is CECAP06T(=LMG 21955T=CECT 5831T).