bluuebunny/crossref_metadata_2025 huggingface dataset:
Russian blues reveal effects of language on color discrimination
Authors: Winawer Jonathan , Witthoft Nathan , Frank Michael C. , Wu Lisa , Wade Alex R. , Boroditsky Lera
Published: May 2007

English and Russian color terms divide the color spectrum differently. Unlike English, Russian makes an obligatory distinction between lighter blues (“goluboy”) and darker blues (“siniy”). We investigated whether this linguistic difference leads to differences in color discrimination. We tested English and Russian speakers in a speeded color discrimination task using blue stimuli that spanned the siniy/goluboy border. We found that Russian speakers were faster to discriminate two colors when they fell into different linguistic categories in Russian (one siniy and the other goluboy) than when they were from the same linguistic category (both siniy or both goluboy). Moreover, this category advantage was eliminated by a verbal, but not a spatial, dual task. These effects were stronger for difficult discriminations (i.e., when the colors were perceptually close) than for easy discriminations (i.e., when the colors were further apart). English speakers tested on the identical stimuli did not show a category advantage in any of the conditions. These results demonstrate that (i) categories in language affect performance on simple perceptual color tasks and (ii) the effect of language is online (and can be disrupted by verbal interference).
Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry
Authors: Frutos Luis Manuel , Andruniów Tadeusz , Santoro Fabrizio , Ferré Nicolas , Olivucci Massimo
Published: May 2007

The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at ≈60-fs delay, initiates a space saving “asynchronous bicycle-pedal or crankshaft” motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy.
PACT is a negative regulator of p53 and essential for cell growth and embryonic development
Authors: Li Li , Deng Binwei , Xing Guichun , Teng Yan , Tian Chunyan , Cheng Xuan , Yin Xiushan , Yang Juntao , Gao Xue , Zhu Yunping , Sun Qihong , Zhang Lingqiang , Yang Xiao , He Fuchu
Published: May 2007

The tumor suppressor p53 regulates cell cycle progression and apoptosis in response to various types of stress, whereas excess p53 activity creates unwanted effects. Tight regulation of p53 is essential for maintaining normal cell growth. p53-associated cellular protein-testes derived (PACT, also known as P2P-R, RBBP6) is a 250-kDa Ring finger-containing protein that can directly bind to p53. PACT is highly up-regulated in esophageal cancer and may be a promising target for immunotherapy. However, the physiological role of the PACT–p53 interaction remains largely unclear. Here, we demonstrate that the disruption of PACT in mice leads to early embryonic lethality before embryonic day 7.5 (E7.5), accompanied by an accumulation of p53 and widespread apoptosis. p53-null mutation partially rescues the lethality phenotype and prolonged survival to E11.5. Endogenous PACT can interact with Hdm2 and enhance Hdm2-mediated ubiquitination and degradation of p53 as a result of the increase of the p53–Hdm2 affinity. Consequently, PACT represses p53-dependent gene transcription. Knockdown of PACT significantly attenuates the p53–Hdm2 interaction, reduces p53 polyubiquitination, and enhances p53 accumulation, leading to both apoptosis and cell growth retardation. Taken together, our data demonstrate that the PACT–p53 interaction plays a critical role in embryonic development and tumorigenesis and identify PACT as a member of negative regulators of p53.
Controlling hydrogelation kinetics by peptide design for three-dimensional encapsulation and injectable delivery of cells
Authors: Haines-Butterick Lisa , Rajagopal Karthikan , Branco Monica , Salick Daphne , Rughani Ronak , Pilarz Matthew , Lamm Matthew S. , Pochan Darrin J. , Schneider Joel P.
Published: May 2007

A peptide-based hydrogelation strategy has been developed that allows homogenous encapsulation and subsequent delivery of C3H10t1/2 mesenchymal stem cells. Structure-based peptide design afforded MAX8, a 20-residue peptide that folds and self-assembles in response to DMEM resulting in mechanically rigid hydrogels. The folding and self-assembly kinetics of MAX8 have been tuned so that when hydrogelation is triggered in the presence of cells, the cells become homogeneously impregnated within the gel. A unique characteristic of these gel–cell constructs is that when an appropriate shear stress is applied, the hydrogel will shear-thin resulting in a low-viscosity gel. However, after the application of shear has stopped, the gel quickly resets and recovers its initial mechanical rigidity in a near quantitative fashion. This property allows gel/cell constructs to be delivered via syringe with precision to target sites. Homogenous cellular distribution and cell viability are unaffected by the shear thinning process and gel/cell constructs stay fixed at the point of introduction, suggesting that these gels may be useful for the delivery of cells to target biological sites in tissue regeneration efforts.
Analysis of the apoptotic and therapeutic activities of histone deacetylase inhibitors by using a mouse model of B cell lymphoma
Authors: Lindemann R. K. , Newbold A. , Whitecross K. F. , Cluse L. A. , Frew A. J. , Ellis L. , Williams S. , Wiegmans A. P. , Dear A. E. , Scott C. L. , Pellegrini M. , Wei A. , Richon V. M. , Marks Paul A. , Lowe S. W. , Smyth M. J. , Johnstone R. W.
Published: May 2007

Histone deacetylase inhibitors (HDACi) can elicit a range of biological responses that affect tumor growth and survival, including inhibition of cell cycle progression, induction of tumor cell-selective apoptosis, suppression of angiogenesis, and modulation of immune responses, and show promising activity against hematological malignancies in clinical trials. Using the Eμ-myc model of B cell lymphoma, we screened tumors with defined genetic alterations in apoptotic pathways for therapeutic responsiveness to the HDACi vorinostat. We demonstrated a direct correlation between induction of tumor cell apoptosis
in vivo
and therapeutic efficacy. Vorinostat did not require p53 activity or a functional death receptor pathway to kill Eμ-myc lymphomas and mediate a therapeutic response but depended on activation of the intrinsic apoptotic pathway with the proapoptotic BH3-only proteins Bid and Bim playing an important role. Our studies provide important information regarding the mechanisms of action of HDACi that have broad implications regarding stratification of patients receiving HDACi therapy alone or in combination with other anticancer agents.
Seco-pregnane steroids target the subgenomic RNA of alphavirus-like RNA viruses
Authors: Li Yanmei , Wang Lihua , Li Shunlin , Chen Xiaoying , Shen Yuemao , Zhang Zhongkai , He Hongping , Xu Wenbo , Shu Yuelong , Liang Guodong , Fang Rongxiang , Hao Xiaojiang
Published: May 2007

Plants have evolved multiple mechanisms to selectively suppress pathogens by production of secondary metabolites with antimicrobial activities. Therefore, direct selections for antiviral compounds from plants can be used to identify new agents with potent antiviral activity but not toxic to hosts. Here, we provide evidence that a class of compounds,seco-pregnane steroid glaucogenin C and its monosugar-glycoside cynatratoside A ofStrobilanthes cusiaand three new pantasugar-glycosides of glaucogenin C ofCynanchum paniculatum, are effective and selective inhibitors to alphavirus-like positive-strand RNA viruses including plant-infecting tobacco mosaic virus (TMV) and animal-infecting Sindbis virus (SINV), eastern equine encephalitis virus, and Getah virus, but not to other RNA or DNA viruses, yet they were not toxic to host cells.In vivoadministration of the compounds protected BALB/c mice from lethal SINV infection without adverse effects on the mice. Using TMV and SINV as models, studies on the action mechanism revealed that the compounds predominantly suppress the expression of viral subgenomic RNA(s) without affecting the accumulation of viral genomic RNA. Our work suggested that the viral subgenomic RNA could be a new target for the discovery of antiviral drugs, and thatseco-pregnane steroid and its four glycosides found in the two medicinal herbs have the potential for further development as antiviral agents against alphavirus-like positive-strand RNA viruses.
Hyperfluidization-coupled membrane microdomain reorganization is linked to activation of the heat shock response in a murine melanoma cell line
Authors: Nagy Enikő , Balogi Zsolt , Gombos Imre , Åkerfelt Malin , Björkbom Anders , Balogh Gábor , Török Zsolt , Maslyanko Andriy , Fiszer-Kierzkowska Anna , Lisowska Katarzyna , Slotte Peter J. , Sistonen Lea , Horváth Ibolya , Vígh László
Published: May 2007

Targeting of the Hsp function in tumor cells is currently being assessed as potential anticancer therapy. An improved understanding of the molecular signals that trigger or attenuate the stress protein response is essential for advances to be made in this field. The present study provides evidence that the membrane fluidizer benzyl alcohol (BA), a documented nondenaturant, acts as a chaperone inducer in B16(F10) melanoma cells. It is demonstrated that this effect relies basically on heat shock transcription factor 1 (HSF1) activation. Under the conditions tested, the BA-induced Hsp response involves the up-regulation of a subset of
hsp
genes. It is shown that the same level of membrane fluidization (estimated in the core membrane region) attained with the closely analogous phenethyl alcohol (PhA) does not generate a stress protein signal. BA, at a concentration that activates heat shock genes, exerts a profound effect on the melting of raft-like cholesterol-sphingomyelin domains
in vitro
, whereas PhA, at a concentration equipotent with BA in membrane fluidization, has no such effect. Furthermore, through the
in vivo
labeling of melanoma cells with a fluorescein labeled probe that inserts into the cholesterol-rich membrane domains [fluorescein ester of polyethylene glycol-derivatized cholesterol (fPEG-Chol)], we found that, similarly to heat stress
per se
, BA, but not PhA, initiates profound alterations in the plasma membrane microdomain structure. We suggest that, apart from membrane hyperfluidization in the deep hydrophobic region, a distinct reorganization of cholesterol-rich microdomains may also be required for the generation and transmission of stress signals to activate
hsp
genes.
A semiquinone intermediate generated at the Q
o
site of the cytochrome
bc
1
complex: Importance for the Q-cycle and superoxide production
Authors: Cape Jonathan L. , Bowman Michael K. , Kramer David M.
Published: May 2007

The cytochrome
bc
1
and related complexes are essential energy-conserving components of mitochondrial and bacterial electron transport chains. They orchestrate a complex sequence of electron and proton transfer reactions resulting in the oxidation of quinol, the reduction of a mobile electron carrier, and the translocation of protons across the membrane to store energy in an electrochemical proton gradient. The enzyme can also catalyze substantial rates of superoxide production, with deleterious physiological consequences. Progress on understanding these processes has been hindered by the lack of observable enzymatic intermediates. We report the first direct detection of a semiquinone radical generated by the Q
o
site using continuous wave and pulsed EPR spectroscopy. The radical is a ubisemiquinone anion and is sensitive to both specific inhibitors and mutations within the Q
o
site as well as O
2
, suggesting that it is the elusive intermediate responsible for superoxide production. Paramagnetic interactions show that the new semiquinone species is buried in the protein, probably in or near the Q
o
site but not strongly interacting with the 2Fe2S cluster. The semiquinone is substoichiometric, even with conditions optimized for its accumulation, consistent with recently proposed models where the semiquinone is destabilized to limit superoxide production. The discovery of this intermediate provides a critical tool to directly probe the elusive chemistry that takes place within the Q
o
site.
Ape gestures and language evolution
Authors: Pollick Amy S. , de Waal Frans B. M.
Published: May 2007

The natural communication of apes may hold clues about language origins, especially because apes frequently gesture with limbs and hands, a mode of communication thought to have been the starting point of human language evolution. The present study aimed to contrast brachiomanual gestures with orofacial movements and vocalizations in the natural communication of our closest primate relatives, bonobos (
Pan paniscus
) and chimpanzees (
Pan troglodytes
). We tested whether gesture is the more flexible form of communication by measuring the strength of association between signals and specific behavioral contexts, comparing groups of both the same and different ape species. Subjects were two captive bonobo groups, a total of 13 individuals, and two captive chimpanzee groups, a total of 34 individuals. The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously. Moreover, bonobos showed greater flexibility in this regard than chimpanzees and were also the only species in which multimodal communication (i.e., combinations of gestures and facial/vocal signals) added to behavioral impact on the recipient.
Regulated proteolysis controls mucoid conversion in
Pseudomonas aeruginosa
Authors: Qiu Dongru , Eisinger Vonya M. , Rowen Donald W. , Yu Hongwei D.
Published: May 2007

Overproduction of the exopolysaccharide alginate causes mucoid conversion in
Pseudomonas aeruginosa
and is a poor prognosticator in cystic fibrosis. The ECF σ factor AlgU and its cognate anti-σ factor MucA are two principal regulators of alginate production. Here, we report the identification of three positive regulators of alginate biosynthesis: PA4033 (designated
mucE
), PA3649 (designated
mucP
), and
algW
. MucE, a small protein (9.5 kDa), was identified as part of a global
mariner
transposon screen for new regulators of alginate production. A transposon located in its promoter caused the overexpression of MucE and mucoid conversion in
P. aeruginosa
strains PAO1 and PA14. Accumulation of MucE in the envelope resulted in increased AlgU activity and reduced MucA levels. Three critical amino acid residues at the C terminus of MucE (WVF) were required for mucoid conversion via two predicted proteases AlgW (DegS) and MucP (RseP/YaeL). Moreover, as in
Escherichia coli
, the PDZ domain of AlgW was required for signal transduction. These results suggest that AlgU is regulated similarly to
E. coli
σ
E
except that the amino acid triad signals from MucE and other envelope proteins that activate AlgW are slightly different from those activating DegS.
Population genetic structure of
Plasmodium falciparum
in the two main African vectors,
Anopheles gambiae
and
Anopheles funestus
Authors: Annan Zeinab , Durand Patrick , Ayala Francisco J. , Arnathau Céline , Awono-Ambene Parfait , Simard Frédéric , Razakandrainibe Fabien G. , Koella Jacob C. , Fontenille Didier , Renaud François
Published: May 2007

We investigated patterns of genetic diversity of
Plasmodium falciparum
associated with its two main African vectors:
Anopheles gambiae
and
Anopheles funestus
. We dissected 10,296 wild-caught mosquitoes from three tropical sites, two in Cameroon (Simbock and Tibati, separated by 320 km) and one in Kenya (Rota, >2,000 km from the other two sites). We assayed seven microsatellite loci in 746 oocysts from 183 infected mosquito guts. Genetic polymorphism was very high in parasites isolated from both vector species. The expected heterozygosity (
H
E
) was 0.79 in both species; the observed heterozygosities (
H
O
) were 0.32 in
A. funestus
and 0.42 in
A. gambiae
, indicating considerable inbreeding within both vector species. Mean selfing (
s
) between genetically identical gametes was
s
= 0.33. Differences in the rate of inbreeding were statistically insignificant among sites and between the two vector species. As expected, because of the high rate of inbreeding, linkage disequilibrium was very high; it was significant for all 21 loci pairs in
A. gambiae
and for 15 of 21 pairs in
A. funestus
, although only two pairwise comparisons were between loci on the same chromosome. Overall, the genetic population structure of
P. falciparum
, as evaluated by
F
statistics, was predominantly clonal rather than panmictic, a population structure that facilitates the spread of antimalarial drug and vaccine resistance and thus may impair the effectiveness of malaria control efforts.
Reliability of oculomotor command signals carried by individual neurons
Authors: Hu Xintian , Jiang Huihui , Gu Chaoliang , Li Chuanyu , Sparks David L.
Published: May 2007

The responses of sensory neurons to repeated presentations of identical stimuli can be highly reproducible. Little is known about the reliability of the motor command signals carried by individual premotor neurons. We measured the variability in the interspike intervals of the high-frequency, saccade-related bursts generated by neurons in the pontine reticular formation. During movements having similar amplitudes and velocity profiles, the interspike intervals of the high-frequency component of the bursts are very similar. The low variability in interspike intervals cannot be attributed to a burst mode characterized by fixed interspike times. Different, but repeatable, burst patterns are observed when movements having approximately the same amplitude but different velocity profiles occur. These findings suggest that the discharge of a single pontine cell is strongly correlated with the activity of other pontine burst cells. Both the high temporal precision of the saccade-related bursts and the correlated activity of pontine burst cells reduce variability in the signals sent to the motoneuron pools and, thereby, contribute to the accuracy and precision of saccadic eye movements.
The importance of fluctuations in fluid mixing
Authors: Kadau Kai , Rosenblatt Charles , Barber John L. , Germann Timothy C. , Huang Zhibin , Carlès Pierre , Alder Berni J.
Published: May 2007

A ubiquitous example of fluid mixing is the Rayleigh–Taylor instability, in which a heavy fluid initially sits atop a light fluid in a gravitational field. The subsequent development of the unstable interface between the two fluids is marked by several stages. At first, each interface mode grows exponentially with time before transitioning to a nonlinear regime characterized by more complex hydrodynamic mixing. Unfortunately, traditional continuum modeling of this process has generally been in poor agreement with experiment. Here, we indicate that the natural, random fluctuations of the flow field present in any fluid, which are neglected in continuum models, can lead to qualitatively and quantitatively better agreement with experiment. We performed billion-particle atomistic simulations and magnetic levitation experiments with unprecedented control of initial interface conditions. A comparison between our simulations and experiments reveals good agreement in terms of the growth rate of the mixing front as well as the new observation of droplet breakup at later times. These results improve our understanding of many fluid processes, including interface phenomena that occur, for example, in supernovae, the detachment of droplets from a faucet, and ink jet printing. Such instabilities are also relevant to the possible energy source of inertial confinement fusion, in which a millimeter-sized capsule is imploded to initiate nuclear fusion reactions between deuterium and tritium. Our results suggest that the applicability of continuum models would be greatly enhanced by explicitly including the effects of random fluctuations.
Cofilin promotes stimulus-induced lamellipodium formation by generating an abundant supply of actin monomers
Authors: Kiuchi Tai , Ohashi Kazumasa , Kurita Souichi , Mizuno Kensaku
Published: May 2007

Cofilin stimulates actin filament disassembly and accelerates actin filament turnover. Cofilin is also involved in stimulus-induced actin filament assembly during lamellipodium formation. However, it is not clear whether this occurs by replenishing the actin monomer pool, through filament disassembly, or by creating free barbed ends, through its severing activity. Using photoactivatable Dronpa-actin, we show that cofilin is involved in producing more than half of all cytoplasmic actin monomers and that the rate of actin monomer incorporation into the tip of the lamellipodium is dependent on the size of this actin monomer pool. Finally, in cofilin-depleted cells, stimulus-induced actin monomer incorporation at the cell periphery is attenuated, but the incorporation of microinjected actin monomers is not. We propose that cofilin contributes to stimulus-induced actin filament assembly and lamellipodium extension by supplying an abundant pool of cytoplasmic actin monomers.
Bax/Bak promote sumoylation of DRP1 and its stable association with mitochondria during apoptotic cell death
Authors: Wasiak Sylwia , Zunino Rodolfo , McBride Heidi M.
Published: May 2007

Dynamin-related protein 1 (DRP1) plays an important role in mitochondrial fission at steady state and during apoptosis. Using fluorescence recovery after photobleaching, we demonstrate that in healthy cells, yellow fluorescent protein (YFP)–DRP1 recycles between the cytoplasm and mitochondria with a half-time of 50 s. Strikingly, during apoptotic cell death, YFP-DRP1 undergoes a transition from rapid recycling to stable membrane association. The rapid cycling phase that characterizes the early stages of apoptosis is independent of Bax/Bak. However, after Bax recruitment to the mitochondrial membranes but before the loss of mitochondrial membrane potential, YFP-DRP1 becomes locked on the membrane, resulting in undetectable fluorescence recovery. This second phase in DRP1 cycling is dependent on the presence of Bax/Bak but independent of hFis1 and mitochondrial fragmentation. Coincident with Bax activation, we detect a Bax/Bak-dependent stimulation of small ubiquitin-like modifier-1 conjugation to DRP1, a modification that correlates with the stable association of DRP1 with mitochondrial membranes. Altogether, these data demonstrate that the apoptotic machinery regulates the biochemical properties of DRP1 during cell death.
Genetic alteration of endothelial heparan sulfate selectively inhibits tumor angiogenesis
Authors: Fuster Mark M. , Wang Lianchun , Castagnola Janice , Sikora Lyudmila , Reddi Krisanavane , Lee Phillip H.A. , Radek Katherine A. , Schuksz Manuela , Bishop Joseph R. , Gallo Richard L. , Sriramarao P. , Esko Jeffrey D.
Published: May 2007

To examine the role of endothelial heparan sulfate during angiogenesis, we generated mice bearing an endothelial-targeted deletion in the biosynthetic enzyme N-acetylglucosamine N-deacetylase/N-sulfotransferase 1 (Ndst1). Physiological angiogenesis during cutaneous wound repair was unaffected, as was growth and reproductive capacity of the mice. In contrast, pathological angiogenesis in experimental tumors was altered, resulting in smaller tumors and reduced microvascular density and branching. To simulate the angiogenic environment of the tumor, endothelial cells were isolated and propagated in vitro with proangiogenic growth factors. Binding of FGF-2 and VEGF164 to cells and to purified heparan sulfate was dramatically reduced. Mutant endothelial cells also exhibited altered sprouting responses to FGF-2 and VEGF164, reduced Erk phosphorylation, and an increase in apoptosis in branching assays. Corresponding changes in growth factor binding to tumor endothelium and apoptosis were also observed in vivo. These findings demonstrate a cell-autonomous effect of heparan sulfate on endothelial cell growth in the context of tumor angiogenesis.
The beginning of kinesin's force-generating cycle visualized at 9-Å resolution
Authors: Sindelar Charles V. , Downing Kenneth H.
Published: May 2007

We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in “ejecting” adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the “neck linker”). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself.
Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA
Authors: Reddy G. S. N. , Garcia-Pichel Ferran
Published: May 2007

Two bacterial strains, CP173-2Tand CP1DT, were isolated from biological soil crusts (BSCs) collected in the Colorado Plateau, USA. Both strains were pigmented, Gram-negative, non-motile rods and produced abundant mucus. They contained C16 : 0, C18 : 1ω7cand C14 : 02-OH as the predominant cellular fatty acids, ubiquinone-10 as the isoprenoid quinone and sphingoglycolipid. Based on the above characteristics, the isolates were assigned to the familySphingomonadaceae; 16 rRNA gene signature nucleotides placed them within the genusSphingomonas. Strains CP173-2Tand CP1DThad a 16S rRNA gene sequence similarity of 96.7 % with each other and 91.6–98.9 % sequence similarity with other species in the genus, indicating that they represent two separate, and possibly novel, species. The closest species to strains CP173-2Tand CP1DTwere, respectively,Sphingomonas dokdonensis(98.9 % gene sequence similarity) andSphingomonas panni(97.9 %). However, strain CP173-2Texhibited a DNA–DNA relatedness of only 32.5 % with the type strain ofS. dokdonensis. Similarly, the DNA–DNA relatedness between strain CP1DTand the type strain ofS. panniwas only 18 %. Phenotypic characterization supported this low relatedness. On the basis of this evidence, we propose that the new strains represent two novel species, for which the namesSphingomonas mucosissimasp. nov. (with type strain CP173-2T=ATCC BAA-1239T=DSM 17494T) andSphingomonas desiccabilissp. nov. (with type strain CP1DT=ATCC BAA-1041T=DSM 16792T) are proposed.
Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium
Authors: Arahal David R. , Lekunberri Itziar , González José M. , Pascual Javier , Pujalte María J. , Pedrós-Alió Carlos , Pinhassi Jarone
Published: May 2007

A Gram-negative, slightly halophilic, strictly aerobic, motile chemoorganotrophic bacterium, strain MED92T, was isolated from a surface water sample from the eastern Mediterranean Sea. Phylogenetic analysis based on its 16S rRNA gene sequence, retrieved from the whole-genome sequence, demonstrated that this isolate is unique, showing <93 % sequence similarity to species of the families Oceanospirillaceae and Alteromonadaceae. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophospholipid and diphosphatidylglycerol. Major fatty acids are 16 : 1ω7c/15 iso 2-OH (41.2 % relative amount), 18 : 1ω7c (35.9 %), 16 : 0 (16.1 %), 10 : 0 3-OH (5.0 %) and 18 : 0 (1.0 %). Preferred carbon sources are organic acids and amino acids. The DNA G+C content is 46.6 mol%. Based on a phenotypic, chemotaxonomic and phylogenetic analyses, it is proposed that this marine bacterium represents a novel genus and species, for which the name Neptuniibacter caesariensis gen. nov., sp. nov. is proposed. The type strain is MED92T (=CECT 7075T=CCUG 52065T).
Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance
Authors: Rahalkar Monali , Bussmann Ingeborg , Schink Bernhard
Published: May 2007

A novel methanotroph, strain LC 2T, was isolated from the littoral sediment of Lake Constance by enrichment in opposing gradients of methane and oxygen, followed by traditional isolation methods. Strain LC 2T grows on methane or methanol as its sole carbon and energy source. It is a Gram-negative, non-motile, pale-pink-coloured methanotroph showing typical intracytoplasmic membranes arranged in stacks. Cells are coccoid, elliptical or rod-shaped and occur often in pairs. Strain LC 2T grows at low oxygen concentrations and in counter-gradients of methane and oxygen. It can grow on medium free of bound nitrogen, possesses the nifH gene and fixes atmospheric nitrogen at low oxygen pressure. It grows at neutral pH and at temperatures between 10 and 30 °C. Phylogenetically, it is most closely related to the genus Methylobacter, with the type strains of Methylobacter tundripaludum and Methylobacter psychrophilus showing 94 and 93.4 % 16S rRNA gene sequence similarity, respectively. Furthermore, the pmoA gene sequence of strain LC 2T is most closely related to pmoA gene sequences of Methylobacter strains (92 % similar to Methylobacter sp. LW 12 by deduced amino acid sequence identity). The DNA G+C content is 49.9 mol% and the major cellular fatty acid is 16 : 1ω7c (60 %). Strain LC 2T (=JCM 14076T=DSM 18750T) is described as the type strain of a novel species within a new genus, Methylosoma difficile gen. nov., sp. nov.
Chromobacterium subtsugae sp. nov., a betaproteobacterium toxic to Colorado potato beetle and other insect pests
Authors: Martin Phyllis A. W. , Gundersen-Rindal Dawn , Blackburn Michael , Buyer Jeffrey
Published: May 2007

Strain PRAA4-1T, a motile, Gram-negative, violet-pigmented bacterium, was isolated from Maryland forest soil and found to be orally toxic to Colorado potato beetle larvae and other insects. Morphological, biological, biochemical and molecular characterization revealed that this strain was most similar to Chromobacterium violaceum, the type species and only currently recognized member of the genus Chromobacterium. DNA–DNA hybridization with C. violaceum ATCC 12472T was 27 %. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain PRAA4-1T and Chromobacterium violaceum form a monophyletic clade, with the closest ancestral taxon Vogesella indigofera within the Betaproteobacteria. On the basis of phenotypic, genotypic and phylogenetic analyses, strain PRAA4-1T (=NRRL B-30655T=DSM 17043T) is proposed as the type strain of a novel species of the genus Chromobacterium, Chromobacterium subtsugae sp. nov.
Hydrogenophaga caeni sp. nov., isolated from activated sludge
Authors: Chung Bok Sil , Ryu Seung Hyun , Park Minjeong , Jeon Yeji , Chung Young Ryun , Jeon Che Ok
Published: May 2007

A Gram-negative bacterium, designated strain EMB71T, was isolated from activated sludge used for enhanced biological phosphorus removal in a sequencing batch reactor. The cells of the isolate were facultatively aerobic, motile rods with single polar flagella. Growth was observed to occur at 15–35 °C (optimally at 30 °C) and at pH 6.0–9.0 (optimally at pH 7.0–8.0). The predominant fatty acids of strain EMB71T were C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH), and the polar lipids comprised a large amount of phosphatidylethanolamine and a small amount of diphosphatidylglycerol. The G+C content of the genomic DNA was 61.6 mol % and the major quinone was Q-8. Comparative 16S rRNA gene sequence analyses showed that strain EMB71T formed a phyletic lineage with the genus Hydrogenophaga within the family Comamonadaceae. The levels of 16S rRNA gene sequence similarity with respect to the type strains of Hydrogenophaga species ranged from 95.1 to 96.9 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB71T represents a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga caeni sp. nov. is proposed. The type strain is EMB71T (=KCTC 12613T=DSM 17962T).
Bacillus selenatarsenatis sp. nov., a selenate- and arsenate-reducing bacterium isolated from the effluent drain of a glass-manufacturing plant
Authors: Yamamura Shigeki , Yamashita Mitsuo , Fujimoto Noriyuki , Kuroda Masashi , Kashiwa Masami , Sei Kazunari , Fujita Masanori , Ike Michihiko
Published: May 2007

A facultatively anaerobic, selenate- and arsenate-reducing bacterium, designated strain SF-1T, was isolated from a selenium-contaminated sediment obtained from an effluent drain of a glass-manufacturing plant in Japan. The bacterium stained Gram-positive and was a motile, spore-forming rod capable of respiring with selenate, arsenate and nitrate as terminal electron acceptors. The major cellular fatty acids of the strain were iso-C15 : 0, iso-C17 : 1
ω10c and C16 : 1
ω7c alcohol. The G+C content of the genomic DNA was 42.8 mol%. Though the nearest phylogenetic neighbour was Bacillus jeotgali JCM 10885T, with a 16S rRNA gene sequence similarity of 99.6 %, DNA–DNA hybridization studies showed only 14 % relatedness between these strains, a level that is clearly below the value recommended to delimit different species. This, together with the phenotypic differences (utilization of electron acceptors, NaCl tolerance), suggests that strain SF-1T represents a novel species of the genus Bacillus, for which the name Bacillus selenatarsenatis sp. nov. is proposed. The type strain is SF-1T (=JCM 14380T=DSM 18680T).
Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid
Authors: Cámara Beatriz , Strömpl Carsten , Verbarg Susanne , Spröer Cathrin , Pieper Dietmar H. , Tindall Brian J.
Published: May 2007

Three bacterial strains, designated MT1T, RW10Tand IpA-2T, had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genusPseudomonas. Analysis of the results of DNA–DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA–DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the namesPseudomonas reinekeisp. nov. (type strain MT1T=DSM 18361T=CCUG 53116T),Pseudomonas mooreisp. nov. (type strain RW10T=DSM 12647T=CCUG 53114T) andPseudomonas mohniisp. nov. (type strain IpA-2T=DSM 18327T=CCUG 53115T) are proposed.
Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea
Authors: Yong Jeong-Joong , Park Soo-Je , Kim Hyeon-Ju , Rhee Sung-Keun
Published: May 2007

A taxonomic study was carried out on an isolate, strain NO2T, from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Gammaproteobacteria and was most closely related to Glaciecola mesophila KMM 241T and Glaciecola polaris LMG 21857T (98.6 and 98.0 % 16S rRNA gene sequence similarity, respectively). The isolate was Gram-negative, aerobic and slightly halophilic and grew in 2–8 % NaCl and at 7–30 °C. Strain NO2T shared some physiological and biochemical properties with G. mesophila KMM 241T and G. polaris LMG 21857T. The G+C content of the genomic DNA of strain NO2T was 45 mol%. Strain NO2T possessed C16 : 0, summed feature 4 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) and summed feature 7 (C18 : 1
ω9c/ω12t/ω7c) as the major cellular fatty acids. DNA–DNA relatedness data indicated that strain NO2T represents a distinct species that is separate from G. mesophila and G. polaris. On the basis of polyphasic evidence, it is proposed that strain NO2T (=KCTC 12755T=LMG 23762T) represents the type strain of a novel species, Glaciecola agarilytica sp. nov.
Chimaereicella boritolerans sp. nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil
Authors: Ahmed Iftikhar , Yokota Akira , Fujiwara Toru
Published: May 2007

A non-motile, Gram-negative, boron-tolerant and alkaliphilic bacterium was isolated from soil of the Hisarcik area in the Kutahya Province of Turkey that was naturally high in boron minerals. The novel isolate, designated T-22T, formed rod-shaped cells, was catalase- and oxidase-positive and tolerated up to 300 mM boron. The strain also survived on agar medium containing up to 3 % (w/v) NaCl. The pH range for growth of this strain was 6.5–10.0 (optimum pH 8.0–9.0) and the temperature range was 16–37 °C (optimum 28–30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed a clear affiliation with the genusChimaereicella, with 97.4 % sequence similarity toChimaereicella alkaliphilaAC-74T, which was the highest similarity among cultivated bacteria. The DNA–DNA relatedness withC. alkaliphilaAC-74Twas 28.3 %. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 03-OH and summed feature 3 (iso-C15 : 02-OH and/or iso-C16 : 1ω7c). The DNA G+C content was 42.5 mol%. Based on the phylogenetic analysis and physiological, chemotaxonomic and genetic data, we concluded that strain T-22Tshould be classified in the genusChimaereicella, and we propose the nameChimaereicella boritoleranssp. nov. for this novel species. The type strain is strain T-22T(=DSM 17298T=NBRC 101277T=ATCC BAA-1189T).
Flavobacterium terrigena sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Jung-Sook , Oh Tae-Kwang
Published: May 2007

A Gram-negative, rod-shaped, Flavobacterium-like bacterial strain, DS-20T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-20T grew optimally at pH 6.5–7.0 and 25 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1
ω9c as the major fatty acids. The DNA G+C content was 38.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-20T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-20T and the type strains of recognized Flavobacterium species were below 94.9 %. Strain DS-20T differed from phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of its phenotypic and phylogenetic distinctiveness, strain DS-20T was classified in the genus Flavobacterium as representing a novel species, for which the name Flavobacterium terrigena sp. nov. is proposed. The type strain is DS-20T (=KCTC 12761T=DSM 17934T).
‘Candidatus Aquirestis calciphila’ and ‘Candidatus Haliscomenobacter calcifugiens’, filamentous, planktonic bacteria inhabiting natural lakes
Authors: Hahn Martin W. , Schauer Michael
Published: May 2007

Filamentous bacteria frequently occurring in the pelagic zone of natural freshwater lakes and ponds were previously identified as being related to Haliscomenobacter hydrossis based upon their 16S rRNA gene sequences. These bacteria exhibit a specific morphology characterized by the formation of straight, stick-like filaments of variable length (5 to >100 μm) and quite stable, but narrow, width (0.25 to 0.35 μm). Bacteria with these morphological characteristics form a monophyletic but broad phylogenetic group with a maximal divergence of 16S rRNA gene sequences of 12.0 %. This monophyletic group consists of at least three monophyletic subclusters. H. hydrossis is affiliated to one of these subclusters and represents the sole recognized species affiliated to the broad monophyletic group. ‘Candidatus Haliscomenobacter calcifugiens' and ‘Candidatus Aquirestis calciphila’ are uncultured representatives of the other two subclusters and have 16S rRNA gene sequence dissimilarities of 5.4 % and 8.2 %, respectively, with the type strain of H. hydrossis. ‘Candidatus H. calcifugiens' and ‘Candidatus A. calciphila’ have a 16S rRNA gene sequence dissimilarity of 8.5 %. These large ribosomal divergences justify the classification of these environmentally important bacteria as a novel species and a new genus, respectively. Intensive attempts to cultivate these filamentous bacteria have resulted in the establishment of mixed cultures, however, attempts to establish pure cultures have failed.
Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico
Authors: Soto-Ramírez Nelís , Sánchez-Porro Cristina , Rosas Soniris , González Wildaomaris , Quiñones Marian , Ventosa Antonio , Montalvo-Rodríguez Rafael
Published: May 2007

A Gram-negative, short rod to oval-shaped bacterium (strain MW2aT) was isolated from the surface of leaves of the black mangroveAvicennia germinansand subjected to a polyphasic taxonomic study. Strain MW2aTwas moderately halophilic, growing at NaCl concentrations in the range 0–25 % (w/v) with optimum growth at 5 % (w/v) NaCl. Growth occurred at 12–40 °C (optimum, 30–35 °C) and at pH 5.0–9.0 (optimum, pH 7.0–8.0). Strain MW2aTwas strictly aerobic. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genusHalomonas. The closest relative wasHalomonas marisflavi, with 98.6 % 16S rRNA gene sequence similarity. The DNA G+C content of strain MW2aTwas 61.5 mol%, which is in the range of values forHalomonasspecies. DNA–DNA hybridization withH. marisflavishowed a relatedness of 42 % and lower values were obtained with respect to other relatedHalomonasspecies. The major fatty acids were C16 : 0, C19 : 0cycloω8c, C18 : 1ω7cand C12 : 03-OH. Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MW2aTrepresents a novel species within the genusHalomonas. The nameHalomonas avicenniaesp. nov. is proposed, with strain MW2aT(=CECT 7193T=CCM 7396T) as the type strain.
Halomonas gudaonensis sp. nov., isolated from a saline soil contaminated by crude oil
Authors: Wang Ya-Nan , Cai Hua , Yu Su-Lin , Wang Zhi-Yao , Liu Jie , Wu Xiao-Lei
Published: May 2007

Two moderately halophilic strains, SL014B-69Tand SL014B-62A2, were isolated from a saline soil contaminated with crude oil in Gudao in the coastal Shengli oilfield in China; the isolates were Gram-negative, rod-shaped and carried lateral flagella. Growth occurred at NaCl concentrations of 1–20 % (w/v), at temperatures of 10–42 °C and at pH 8.0–9.0. Strain SL014B-69Thad C18 : 1ω7c(28.61 %), C19 : 1cycloω7c(27.97 %), C16 : 0(19.66 %) and C12 : 03-OH (8.87 %) as the predominant fatty acids and Q9 as the major ubiquinone, with the G+C content of genomic DNA being 64.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains belonged to genus ofHalomonasin theGammaproteobacteria, with the highest 16S rRNA gene sequence similarities of 96.4 % withHalomonas campisalisATCC 700597Tand 96.0 % withHalomonas desiderataFB2T. DNA–DNA relatedness of strain SL014B-69Twith strain SL014B-62A2,H. campisalisATCC 700597TandH. desiderataDSM 9502Twas 97.4, 42.9 and 36.8 %, respectively. On the basis of these data, a novel species of the genusHalomonas,Halomonas gudaonensissp. nov., is proposed for strain SL014B-69Tand SL014B-62A2. The type strain is SL014B-69T(=LMG 23610T=CGMCC 1.6133T).
Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family ‘Flammeovirgaceae’ isolated from sediment
Authors: Yoon Jaewoo , Ishikawa Shu , Kasai Hiroaki , Yokota Akira
Published: May 2007

A strictly aerobic, Gram-negative, gliding, dull-orange-pigmented, rod-shaped bacterium, designated strain Shu-F-UV2-2T, was isolated from sediment (Carp Island, Republic of Palau) and was the focus of a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated to the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes and that it showed highest sequence similarity (85.5 %) to Flammeovirga yaeyamensis NBRC 100898T. The novel isolate could be differentiated phenotypically and physiologically from recognized members of the family ‘Flammeovirgaceae’. The G+C content of the DNA was 43.0 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1
ω7c and C16 : 1
ω5c were the major fatty acids. On the basis of this polyphasic evidence, it was concluded that strain Shu-F-UV2-2T represents a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Perexilibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain is Shu-F-UV2-2T (=MBIC06993T=IAM 15413T=KCTC 12867T).
Blastobotrys americana sp. nov., Blastobotrys illinoisensis sp. nov., Blastobotrys malaysiensis sp. nov., Blastobotrys muscicola sp. nov., Blastobotrys peoriensis sp. nov. and Blastobotrys raffinosifermentans sp. nov., novel anamorphic yeast species
Authors: Kurtzman Cletus P.
Published: May 2007

The genus Blastobotrys, which now includes species previously assigned to the synonymous genera Arxula and Sympodiomyces, represents the anamorph of the ascosporogenous genus Trichomonascus. Six novel species are proposed for assignment to Blastobotrys. They were detected from their unique nucleotide sequences in large-subunit rDNA, ITS1–5.8S–ITS2 rDNA, mitochondrial small-subunit rDNA and the cytochrome oxidase II gene. The proposed novel species are Blastobotrys americana sp. nov. (type strain NRRL Y-6844T=CBS 10337T; substrate unknown; Kansas, USA), Blastobotrys illinoisensis sp. nov. (type strain NRRL YB-1343T=CBS 10339T; from forest debris; Illinois, USA), Blastobotrys malaysiensis sp. nov. (type strain NRRL Y-6417T=CBS 10336T; from soil; Malaysia), Blastobotrys muscicola sp. nov. (type strain NRRL Y-7993T=CBS 10338T; from moss; Louisiana, USA), Blastobotrys peoriensis sp. nov. (type strain NRRL YB-2290T=CBS 10340T; from a fungus; Peoria, IL, USA) and Blastobotrys raffinosifermentans sp. nov. (type strain NRRL Y-27150T=CBS 6800T; substrate unknown).