bluuebunny/crossref_metadata_2025 huggingface dataset:
A fast Fourier transform implementation of the Kramers-Kronig relations: Application to anomalous and left handed propagation
Authors: Lucas Jérôme , Géron Emmanuel , Ditchi Thierry , Holé Stéphane
Published: August 2012

In this this paper we quickly derive the Kramers-Kronig relations from simple causality considerations and propose a simple way to implement them using the Fast Fourier Transform. This work focuses on how to make these relations a usable tool even when their conditions of validity are not strictly respected. In this respect we emphasize on their application to the constant low level loss approximation at microwave frequencies. The method presented is demonstrated on various typical cases of fancy propagation: high velocity, negative phase velocity and evanescent waves.
pn-control and pn-homojunction formation of metal-free phthalocyanine by doping
Authors: Shinmura Yusuke , Kubo Masayuki , Ishiyama Norihiro , Kaji Toshihiko , Hiramoto Masahiro
Published: August 2012

The Fermi level (EF) of metal-free phthalocyanine (H2Pc), located at the center of the bandgap (4.4 eV), is shifted to 3.8 eV, close to the conduction band (3.5 eV), by cesium carbonate doping and shifted to 4.9 eV, close to the valence band (5.1 eV), by molybdenum oxide doping under oxygen free conditions. Formation of n- and p-type Schottky junctions and pn-homojunctions in single H2Pc films, confirmed by their photovoltaic properties, clearly demonstrates the formation of n- and p-type H2Pc.
Ultraviolet-visible spectroscopy of graphene oxides
Authors: Lai Qi , Zhu Shifu , Luo Xueping , Zou Min , Huang Shuanghua
Published: August 2012

Dispersions of few-layer (1-3 layers), multi-layer (4-10 layers) and thick-layer (>10 layers) graphene oxide (GO) were prepared by a modified Hummers method with different mass ratios of KMnO4 to graphite. Ultraviolet-visible (UV-vis) spectroscopic data show that few-layer GO dispersions can be distinguished from multi- and thick-layer dispersions by a more intense peak at 230 nm. Atomic force microscopy (AFM) images of few-layer GO contain a single peak, those of multi-layer GO exhibit a shoulder and those of thick-layer GO do not contain a peak or shoulder. These findings allow qualitative analysis of GO dispersions. X-ray photoelectron spectra (XPS) show that the change of UV-vis absorption intensity of GO is caused by a conjugative effect related to chromophore aggregation that influences the π-π* plasmon peak.
Inverse spin Hall effect in ferromagnetic metal with Rashba spin orbit coupling
Authors: Xing M.-J. , Jalil M. B. A. , Tan Seng Ghee , Jiang Y.
Published: August 2012

We report an intrinsic form of the inverse spin Hall effect (ISHE) in ferromagnetic (FM) metal with Rashba spin orbit coupling (RSOC), which is driven by a normal charge current. Unlike the conventional form, the ISHE can be induced without the need for spin current injection from an external source. Our theoretical results show that Hall voltage is generated when the FM moment is perpendicular to the ferromagnetic layer. The polarity of the Hall voltage is reversed upon switching the FM moment to the opposite direction, thus promising a useful reading mechanism for memory or logic applications.
Nitrogen induced ferromagnetism in Cobalt doped BaTiO3
Authors: Mitra Chandrima
Published: August 2012

The electronic structure and magnetism of Cobalt doped BaTiO3 (BaTi1−xCoxO3) is investigated. Substitutional Nitrogen on an Oxygen site is found to play an important role in inducing net magnetic moments in the system. The presence of a Nitrogen atom as nearest neighbour to a Cobalt atom is crucial in producing spin splitting of both the Nitrogen and Cobalt states thereby introducing a net local magnetic moment. The introduction of Nitrogen is further found to enhance ferromagnetic interactions between Cobalt atoms.
Cooperation and assortativity with dynamic partner updating
Authors: Wang Jing , Suri Siddharth , Watts Duncan J.
Published: August 2012

The natural tendency for humans to make and break relationships is thought to facilitate the emergence of cooperation. In particular, allowing conditional cooperators to choose with whom they interact is believed to reinforce the rewards accruing to mutual cooperation while simultaneously excluding defectors. Here we report on a series of human subjects experiments in which groups of 24 participants played an iterated prisoner’s dilemma game where, critically, they were also allowed to propose and delete links to players of their own choosing at some variable rate. Over a wide variety of parameter settings and initial conditions, we found that dynamic partner updating significantly increased the level of cooperation, the average payoffs to players, and the assortativity between cooperators. Even relatively slow update rates were sufficient to produce large effects, while subsequent increases to the update rate had progressively smaller, but still positive, effects. For standard prisoner’s dilemma payoffs, we also found that assortativity resulted predominantly from cooperators avoiding defectors, not by severing ties with defecting partners, and that cooperation correspondingly suffered. Finally, by modifying the payoffs to satisfy two novel conditions, we found that cooperators did punish defectors by severing ties, leading to higher levels of cooperation that persisted for longer.
Structure–function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation
Authors: Quevillon-Cheruel Sophie , Campo Nathalie , Mirouze Nicolas , Mortier-Barrière Isabelle , Brooks Mark A. , Boudes Marion , Durand Dominique , Soulet Anne-Lise , Lisboa Johnny , Noirot Philippe , Martin Bernard , van Tilbeurgh Herman , Noirot-Gros Marie-Françoise , Claverys Jean-Pierre , Polard Patrice
Published: August 2012

Transformation promotes genome plasticity in bacteria via RecA-driven homologous recombination. In the Gram-positive human pathogen
Streptococcus pneumoniae
, the transformasome a multiprotein complex, internalizes, protects, and processes transforming DNA to generate chromosomal recombinants. Double-stranded DNA is internalized as single strands, onto which the transformation-dedicated DNA processing protein A (DprA) ensures the loading of RecA to form presynaptic filaments. We report that the structure of DprA consists of the association of a sterile alpha motif domain and a Rossmann fold and that DprA forms tail-to-tail dimers. The isolation of DprA self-interaction mutants revealed that dimerization is crucial for the formation of nucleocomplexes in vitro and for genetic transformation. Residues important for DprA–RecA interaction also were identified and mutated, establishing this interaction as equally important for transformation. Positioning of key interaction residues on the DprA structure revealed an overlap of DprA–DprA and DprA–RecA interaction surfaces. We propose a model in which RecA interaction promotes rearrangement or disruption of the DprA dimer, enabling the subsequent nucleation of RecA and its polymerization onto ssDNA.
Reinduced Wnt signaling limits regenerative potential of sensory axons in the spinal cord following conditioning lesion
Authors: Hollis Edmund R. , Zou Yimin
Published: August 2012

Conditioning lesion of the peripheral branch of dorsal column axons is a well-known paradigm enabling the central branch to regenerate after injury to the spinal cord. However, only a small number of regenerating axons enter grafted substrates, and they do not grow beyond the lesion. We found that conditioning lesion induces, in addition to growth-stimulating genes, related to receptor tyrosine kinase (Ryk), a potent repulsive receptor for Wnts. Wnts are expressed around the site of spinal cord injury, and we found that grafted bone marrow stromal cells secreting the Wnt inhibitors secreted frizzled-related protein 2 or Wnt inhibitory factor 1 enhanced regeneration of the central branch after peripheral conditioning lesion. Furthermore, we found that Wnt4-expressing grafts caused dramatic long-range retraction of the injured central branch of conditioned dorsal root ganglion neurons. Macrophages accumulate along the path of receding axons but not around Wnt4-expressing cells, suggesting that the retraction of dorsal column axons is not a secondary effect of increased macrophages attracted by Wnt4. Therefore, Wnt-Ryk signaling is an inhibitory force co-induced with growth-stimulating factors after conditioning lesion. Overcoming Wnt inhibition may further enhance therapies being designed on the basis of the conditioning-lesion paradigm.
HIV-1 matrix protein p17 promotes angiogenesis via chemokine receptors CXCR1 and CXCR2
Authors: Caccuri Francesca , Giagulli Cinzia , Bugatti Antonella , Benetti Anna , Alessandri Giulio , Ribatti Domenico , Marsico Stefania , Apostoli Paola , Slevin Mark A. , Rusnati Marco , Guzman Carlos A. , Fiorentini Simona , Caruso Arnaldo
Published: August 2012

Vascular diseases supported by aberrant angiogenesis have increased incidence in HIV-1–infected patients. Several data suggest that endothelium dysfunction relies on action of HIV-1 proteins rather than on a direct effect of the virus itself. The HIV-1 matrix protein p17 is known to deregulate the biological activity of different immune cells. Recently, p17 was found to mimic IL-8 chemokine activity by binding to the IL-8 receptor CXCR1. Here we show that p17 binds with high affinity to CXCR2, a CXCR1-related receptor, and promotes the formation of capillary-like structures on human endothelial cells (ECs) by interacting with both CXCR1 and CXCR2 expressed on the EC surface. ERK signaling via Akt was defined as the pathway responsible for p17-induced tube formation. Ex vivo and in vivo experimental models confirmed the provasculogenic activity of p17, which was comparable to that induced by VEGF-A. The hypothesis of a major role for p17 in HIV-1–induced aberrant angiogenesis is enforced by the finding that p17 is detected, as a single protein, in blood vessels of HIV-1–patients and in particular in the nucleus of ECs. Localization of p17 in the nucleus of ECs was evidenced also in in vitro experiments, suggesting the internalization of exogenous p17 in ECs by mechanisms of receptor-mediated endocytosis. Recognizing p17 interaction with CXCR1 and CXCR2 as the key event in sustaining EC aberrant angiogenesis could help us to identify new treatment strategies in combating AIDS-related vascular diseases.
Nucleic acid-containing amyloid fibrils potently induce type I interferon and stimulate systemic autoimmunity
Authors: Di Domizio Jeremy , Dorta-Estremera Stephanie , Gagea Mihai , Ganguly Dipyaman , Meller Stephan , Li Ping , Zhao Bihong , Tan Filemon K. , Bi Liqi , Gilliet Michel , Cao Wei
Published: August 2012

The immunopathophysiologic development of systemic autoimmunity involves numerous factors through complex mechanisms that are not fully understood. In systemic lupus erythematosus, type I IFN (IFN-I) produced by plasmacytoid dendritic cells (pDCs) critically promotes the autoimmunity through its pleiotropic effects on immune cells. However, the host-derived factors that enable abnormal IFN-I production and initial immune tolerance breakdown are largely unknown. Previously, we found that amyloid precursor proteins form amyloid fibrils in the presence of nucleic acids. Here we report that nucleic acid-containing amyloid fibrils can potently activate pDCs and enable IFN-I production in response to self-DNA, self-RNA, and dead cell debris. pDCs can take up DNA-containing amyloid fibrils, which are retained in the early endosomes to activate TLR9, leading to high IFNα/β production. In mice treated with DNA-containing amyloid fibrils, a rapid IFN response correlated with pDC infiltration and activation. Immunization of nonautoimmune mice with DNA-containing amyloid fibrils induced antinuclear serology against a panel of self-antigens. The mice exhibited positive proteinuria and deposited antibodies in their kidneys. Intriguingly, pDC depletion obstructed IFN-I response and selectively abolished autoantibody generation. Our study reveals an innate immune function of nucleic acid-containing amyloid fibrils and provides a potential link between compromised protein homeostasis and autoimmunity via a pDC-IFN axis.
STIM1 and STIM2 protein deficiency in T lymphocytes underlies development of the exocrine gland autoimmune disease, Sjögren's syndrome
Authors: Cheng Kwong Tai , Alevizos Ilias , Liu Xibao , Swaim Wiliam D. , Yin Hongen , Feske Stefan , Oh-hora Masatsugu , Ambudkar Indu S.
Published: August 2012

Primary Sjögren's Syndrome (pSS) is an autoimmune disease involving salivary and other exocrine glands that leads to progressive lymphocytic infiltration into the gland, tissue damage, and secretory defects. The mechanism underlying this disease remains poorly understood. Here we report that mice with T-cell–targeted deletion of Stromal Interaction Molecule (STIM) 1 and STIM2 [double-knockout (DKO)] mice develop spontaneous and severe pSS-like autoimmune disease, displaying major hallmarks of the disease. In DKO mice, diffuse lymphocytic infiltration was seen in submandibular glands, a major target of pSS, by age 6 wk, progressing to severe inflammation by age 12 wk. Sjögren's syndrome-specific autoantibodies (SSA/Ro and SSB/La) were detected in the serum, and progressive salivary gland destruction and loss of fluid secretion were also seen. Importantly, we report that peripheral blood mononuclear cells as well as lymphocytic infiltrates in submandibular glands from patients with pSS demonstrated significant reductions in STIM1 and STIM2 proteins. Store-operated calcium entry was also reduced in peripheral blood mononuclear cells from pSS patients compared with those from healthy controls. Thus, deficiency of STIM1 and STIM2 proteins in T cells, and consequent defects in Ca2+signaling, are associated with salivary gland autoimmunopathy in DKO mice and pSS patients. These data reveal a previously unreported link between STIM1 and STIM2 proteins and pSS.
A new class of hypercomplex analytic cusp forms
Authors: Constales D. , Grob D. , Kraußhar R.
Published: August 2012

In this paper we deal with a new class of Clifford algebra valued automorphic forms on arithmetic subgroups of the Ahlfors-Vahlen group. The forms that we consider are in the kernel of the operatorDΔk/2D \Delta ^{k/2}for some evenk∈Zk \in {\mathbb {Z}}. They will be calledkk-holomorphic Cliffordian automorphic forms.kk-holomorphic Cliffordian functions are well equipped with many function theoretical tools. Furthermore, the real component functions also have the property that they are solutions to the homogeneous and inhomogeneous Weinstein equations. This function class includes the set ofkk-hypermonogenic functions as a special subset. While we have not been able so far to propose a construction for non-vanishingkk-hypermonogenic cusp forms fork≠0k \neq 0, we are able to do so within this larger set of functions. After having explained their general relation to hyperbolic harmonic automorphic forms, we turn to the construction of Poincaré series. These provide us with non-trivial examples of cusp forms within this function class. Then we establish a decomposition theorem of the spaces ofkk-holomorphic Cliffordian automorphic forms in terms of a direct orthogonal sum of the spaces ofkk-hypermonogenic Eisenstein series and ofkk-holomorphic Cliffordian cusp forms.
Additional Cross-sectional Transesophageal Echocardiography Views Improve Perioperative Right Heart Assessment
Authors: Kasper Jorge , Bolliger Daniel , Skarvan Karl , Buser Peter , Filipovic Miodrag , Seeberger Manfred Daniel
Published: August 2012

Background

Right heart failure is an important cause of perioperative morbidity and mortality, and transesophageal echocardiography (TEE) is crucial for its diagnosis. However, only four of the 20 cross-sectional views recommended in current guidelines for intraoperative TEE focus on the right heart. This study analyzed whether incorporating additional views into the standard TEE examination improves assessment of the right heart.

Methods

Sixty patients underwent standard TEE examination after induction of anesthesia. In addition, five views focusing on the right heart were acquired. Offline analysis tested: (1) whether the additional TEE views can be acquired as reliably as standard views including parts of the right heart; whether incorporating additional views improves the assessment of (2) eight or more right ventricular wall segments based on a predefined nine-segment model; (3) the tricuspid or pulmonary valve in two or more planes; and (4) transvalvular tricuspid and pulmonary flow in orthograde fashion.

Results

Additional views could be imaged as reliably (88%) as standard views (90%). Incorporating some of the additional views allowed the assessment of eight or more right ventricular segments in 59 (98%) versus 18 patients (30%) by the standard views alone, and of the pulmonary valve in two or more planes in 60 (100%) versus 15 patients (25%). Several additional views improved orthograde assessment of transvalvular pulmonary flow, but not of tricuspid flow.

Conclusions

The additional TEE views focusing on the right heart can be acquired as reliably as standard views. Incorporating three of them into the standard TEE examination improves comprehensive assessment of the right heart.
γ-Aminobutyric Acid Receptor Type A Receptor Potentiation Reduces Firing of Neuronal Assemblies in a Computational Cortical Model
Authors: Storer Kingsley P. , Reeke George N.
Published: August 2012

Background

The understanding of how general anesthetics act on individual cells and on global brain function has increased significantly during the last decade. What remains poorly understood is how anesthetics act at intermediate scales. Several major theories emphasize the importance of neuronal groups, sets of strongly connected neurons that fire in a time-locked fashion, in all aspects of brain function, particularly as a necessary substrate of consciousness. The authors have undertaken computer modeling to determine how ã-aminobutyric acid receptor type A (GABAA) receptor potentiating agents such as propofol may influence the dynamics of neuronal group formation and ongoing activity.

Methods

A computer model of a cortical network with connections modified by synaptic plasticity was examined. At baseline, the model spontaneously formed neuronal groups. Direct effects of GABAA receptor potentiation and indirect effects on input drive were then examined to study their effects on this process.

Results

Potentiation of GABAA inhibition and input drive reduction reduced the firing frequency of inhibitory and excitatory neurons in a dose-dependent manner. The diminution in spiking rates led to dramatic reductions in the firing frequency of neuronal groups. Simulated electroencephalographic output from the model at baseline exhibits gamma and theta rhythmicity. The direct and indirect GABAA effects reduce the amplitude of these underlying rhythms and modestly slow the gamma rhythm.

Conclusions

GABAA facilitation both directly and indirectly inhibits the ability of neurons to form groups spontaneously. A lack of group formation is consistent with some theories of anesthetic-induced loss of memory formation and consciousness.
Deficits in Retention for Verbally Presented Medical Information
Authors: Sandberg Elisabeth H. , Sharma Ritu , Sandberg Warren S.
Published: August 2012

Background

Anesthesiologists deliver large quantities of verbal information to patients during preoperative teaching. Basic principles of cognitive psychology dictate that much of this information is likely to be forgotten. Exactly how much and what type of information can be retained and recalled remains an open question.

Methods

With Institutional Review Board approval, 98 healthy, educated volunteers viewed a brief video containing a preoperative explanation of anesthetic options and instructions. Subjects were then asked to engage in free and cued recall of information from the video, and to complete a recognition task. We developed a coding scheme to objectively score the free and cued recall tasks for the quantity of information recalled relative to the quantity presented in the video. Data are presented as descriptive statistics.

Results

Subjects spontaneously recalled less than 25% of the information presented. Providing retrieval cues greatly enhanced recall: Subjects recalled 67%, on average, of the material queried in the cued recall task. Performance was even stronger on the multiple-choice test (83% of items correctly answered), indicating that the information was initially encoded. The category of information that was consistently least-remembered was presurgical medication instructions.

Conclusions

Under realistic conditions for recall, most medical instruction given to patients will not be recalled, even if it is initially encoded. Given the limits of short-term memory, clinicians should carefully consider their patterns of information giving. Improvement of memory performance with cues for retrieval indicates that providing printed instructions for later review may be beneficial.
Epinephrine Induces Rapid Deterioration in Pulmonary Oxygen Exchange in Intact, Anesthetized Rats
Authors: Krishnamoorthy Vijay , Hiller David B. , Ripper Richard , Lin Bocheng , Vogel Stephen M. , Feinstein Douglas L. , Oswald Sarah , Rothschild Leelach , Hensel Priscilla , Rubinstein Israel , Minshall Richard , Weinberg Guy L.
Published: August 2012

Background

Previous studies indicate epinephrine adversely affects arterial oxygenation when administered in a rat model of local anesthetic overdose. The authors tested whether epinephrine alone exerts similar effects in the intact animal.

Methods

Anesthetized rats received a single intravenous injection of epinephrine (25, 50, or 100 mcg/kg); matched cohorts were pretreated with phentolamine (100 mcg/kg); n = 5 for each of the six treatment groups. Arterial pressure and blood gases were measured at baseline, 1 and 10 min after epinephrine administration. Pulmonary capillary pressures during epinephrine infusion with normal and increased flows were measured in an isolated lung preparation.

Results

Epinephrine injection in the intact animal caused hypoxemia, hypercapnia, and acidosis at all doses. Arterial oxygen tension was reduced within 1 min of injection. Hyperlactatemia occurred by 10 min after 50 and 100 mcg/kg. Rate pressure product was decreased by 10 min after 100 mcg/kg epinephrine. Pretreatment with phentolamine attenuated these effects except at 100 mcg/kg epinephrine. In the isolated lung preparation, epinephrine in combination with increased pulmonary flow increased pulmonary capillary pressure and lung water.

Conclusions

Bolus injection of epinephrine in the intact, anesthetized rat impairs pulmonary oxygen exchange within 1 min of treatment. Effects were blunted by α-adrenergic receptor blockade. Edema occurred in the isolated lung above a threshold pulmonary capillary pressure when epinephrine treatment was coupled with an increase in pulmonary flow. These results potentially argue against using traditional doses of epinephrine for resuscitation, particularly in the anesthetized patient.
Wet mammals shake at tuned frequencies to dry
Authors: Dickerson Andrew K. , Mills Zachary G. , Hu David L.
Published: August 2012

In cold wet weather, mammals face hypothermia if they cannot dry themselves. By rapidly oscillating their bodies, through a process similar to shivering, furry mammals can dry themselves within seconds. We use high-speed videography and fur particle tracking to characterize the shakes of 33 animals (16 animals species and five dog breeds), ranging over four orders of magnitude in mass from mice to bears. We here report the power law relationship between shaking frequencyfand body massMto bef∼M−0.22, which is close to our prediction off∼M−0.19based upon the balance of centrifugal and capillary forces. We also observe a novel role for loose mammalian dermal tissue: by whipping around the body, it increases the speed of drops leaving the animal and the ensuing dryness relative to tight dermal tissue.
Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family

Rhodospirillaceae
Authors: Amoozegar Mohammad Ali , Makhdoumi-Kakhki Ali , Ramezani Mohadaseh , Nikou Mahdi Moshtaghi , Fazeli Seyed Abolhassan Shahzadeh , Schumann Peter , Ventosa Antonio
Published: August 2012

A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16T, was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16T were not motile. Growth occurred with 2.5–5.2 M NaCl (optimum 3.4 M), at pH 6.0–8.0 (optimum pH 7.0) and at 30–50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16T belonged in the family

Rhodospirillaceae

and that its closest relatives were

Rhodovibrio sodomensis

DSM 9895T (91.6 % sequence similarity),

Rhodovibrio salinarum

NCIMB 2243T (91.2 %),

Pelagibius litoralis

CL-UU02T (88.9 %) and

Fodinicurvata sediminis

YIM D82T (88.7 %). The novel strain’s major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16T contained the ubiquinone Q-10. The G+C content of the novel strain’s genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16T and other previously described taxa indicate that the strain represents a novel species in a new genus within the family

Rhodospirillaceae

, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16T ( = IBRC-M 10018T  = DSM 25584T).
Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus

Polaribacter

and two

Polaribacter

species
Authors: Fukui Youhei , Abe Mahiko , Kobayashi Masahiro , Saito Hiroaki , Oikawa Hiroshi , Yano Yutaka , Satomi Masataka
Published: August 2012

Three Gram-negative, non-motile, strictly aerobic strains, designated LNM-20T, LCM-1 and LAM-13, were isolated from thalli of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates were associated with the genus

Polaribacter

in the family

Flavobacteriaceae

and were most closely related to

Polaribacter dokdonensis

DSW-5T (96.2 % 16S rRNA gene sequence similarity) and

Polaribacter gangjinensis

K17-16T (95.0 %). The DNA G+C content of the isolates was 28.6–29.2 mol%. DNA–DNA hybridization analysis showed that the isolates belonged to a single species distinct from both of their closest relatives. The only isoprenoid quinone detected was menaquinone-6. The main polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1ω10c and iso-C15 : 0 3-OH. The phenotypic features of strain LNM-20T differed from those of their closest relatives in several regards (colony colour, growth with 1 % NaCl and on TSA plus 2.5 % NaCl, hydrolysis of Tweens 40 and 80, and oxidization of five carbon compounds). On the basis of phylogenetic, chemotaxonomic and phenotypic analysis, the isolates represent a novel species in the genus

Polaribacter

, for which the name Polaribacter porphyrae sp. nov. is proposed. The type strain is LNM-20T ( = LMG 26671T  = NBRC 108759T). Emended descriptions of the genus

Polaribacter

and

P. dokdonensis

and

P. gangjinensis

are also proposed.
Neptunomonas qingdaonensis sp. nov., isolated from intertidal sand
Authors: Liu Ang , Zhang Xi-Ying , Chen Chun-Xiao , Xie Bin-Bin , Qin Qi-Long , Liu Chang , Li Guo-Wei , Li Hai , Xu Zhong , Chen Xiu-Lan , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: August 2012

A Gram-negative, motile, aerobic, oxidase- and catalase-positive rod, designated P10-2-4T, was isolated from an intertidal sand sample collected from a coastal area of Qingdao (Yellow Sea), China. The isolate reduced nitrate to nitrite and grew at 4–33 °C and with 0.5–12 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major respiratory quinone was Q-8. The genomic DNA G+C content was 45.1 %. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain P10-2-4T belonged to the genus

Neptunomonas

. The isolate shared the highest 16S rRNA gene sequence similarity (98.1 %) with

Neptunomonas japonica

JAMM 0745T and 96.9, 96.5 and 95.9 % sequence similarities with

N. antarctica

S3-22T,

N. concharum

LHW37T and

N. naphthovorans

NAG-2N-126T, respectively, strains of the other three recognized species in the genus. DNA–DNA relatedness between strain P10-2-4T and

N. japonica

JCM 14595T was 35.6 %. Furthermore, strain P10-2-4T could be distinguished from the representatives of the genus

Neptunomonas

by a combination of phenotypic characteristics, such as temperature and NaCl concentration for growth, nitrate reduction, DNase activity and assimilation of substrates. The data from this study suggests that strain P10-2-4T represents a novel species in the genus

Neptunomonas

, for which the name Neptunomonas qingdaonensis sp. nov. is proposed. The type strain is P10-2-4T ( = CGMCC 1.10971T  = KCTC 23686T).
Sphingobacterium thermophilum sp. nov., of the phylum

Bacteroidetes

, isolated from compost
Authors: Yabe Shuhei , Aiba Yoshifumi , Sakai Yasuteru , Hazaka Masaru , Kawahara Kazuyoshi , Yokota Akira
Published: August 2012

A Gram-negative bacterium, designated CKTN2T, was isolated from compost. Cells of strain CKTN2T were strictly aerobic rods. The isolate grew at 20–50 °C (optimum 40–45 °C), but not below 15 °C or above 52 °C, and at pH 5.9–8.8 (optimum pH 7.0), but not below pH 5.4 or above pH 9.3. The DNA G+C content was 40.3 mol%. The predominant menaquinone was MK-7. The major fatty acids were iso-C15 : 0 (45.2 %), iso-C17 : 0 3-OH (11.1 %) and C18 : 0 (14.5 %). Analysis of the 16S rRNA gene sequence of strain CKTN2T revealed that it is a member of the genus

Sphingobacterium

and is most closely related to

Sphingobacterium alimentarium

DSM 22362T (93.2 % 16S rRNA gene sequence similarity). Strain CKTN2T could be distinguished from its closest phylogenetic relatives by different phenotypic characteristics. According to the phenotypic and genotypic characteristics, strain CKTN2T represents a novel species of the genus

Sphingobacterium

, for which the name Sphingobacterium thermophilum sp. nov. is proposed. The type strain is CKTN2T ( = JCM 17858T  = KCTC 23708T).
Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga
Authors: Penesyan Anahit , Breider Sven , Schumann Peter , Tindall Brian J. , Egan Suhelen , Brinkhoff Thorsten
Published: August 2012

Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95T, were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the

Roseobacter

clade within the

Alphaproteobacteria

. The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95T were identical (52.6 mol%) and they had a DNA–DNA hybridization value of 83.7 %, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95T was

Thalassobius aestuarii

DSM 15283T with 95.8 % 16S rRNA gene sequence similarity. Other close relatives include further species of the genera

Thalassobius

and

Shimia

. Strains U82 and U95T were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1 %) were 18 : 1ω7c, 16 : 0, 18 : 2, 10 : 0 3-OH, 12 : 0, 20 : 1 2-OH and 18 : 0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95T are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95T ( = DSM 24752T = LMG 26464T).
Neiella marina gen. nov., sp. nov., isolated from the sea cucumber Apostichopus japonicus
Authors: Du Zong-Jun , Miao Ting-Ting , Rooney Alejandro P. , Liu Qian-Qian , Chen Guan-Jun
Published: August 2012

A novel strain, designated J221T, was isolated from the intestine of a sea cucumber, Apostichopus japonicus, collected from earthen ponds in Qingdao, China. The strain was Gram-negative, oxidase-positive, aerobic, rod-shaped and motile by means of one to several polar flagella. Growth of strain J221T was observed at temperatures between 10 and 40 °C with optimum growth between 25 and 28 °C. The pH range for growth was 5.0–9.0 with optimum growth at pH 7.5–8.0. The dominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 29.04 %), C16 : 0 (28.93 %) and C18 : 1ω7c (26.15 %). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Diphosphatidylglycerol, an unknown aminolipid and an unknown aminophospholipid were present in moderate to minor amounts in the polar lipid profile. Strain J221T had Q-8 as the major respiratory quinone. The DNA G+C content of strain J221T was 46.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J221T is a member of the

Gammaproteobacteria

. It formed a distinct phyletic line with less than 91 % sequence similarity to any species within previously recognized genera. On the basis of this polyphasic taxonomic study, strain J221T should be classified as a representative of a novel species of a new genus, for which the name Neiella marina gen. nov., sp. nov. is proposed. The type strain of Neiella marina is J221T ( = CGMCC 1.10130T = NRRL B-51319T).
Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants
Authors: Álvarez-Pérez Sergio , Lievens Bart , Jacquemyn Hans , Herrera Carlos M.
Published: August 2012

The taxonomic status of 14 strains of members of the genus

Acinetobacter

isolated from floral nectar of wild Mediterranean insect-pollinated plants, which did not belong to any previously described species within this genus, was investigated following a polyphasic approach. Confirmation that these strains formed two separate lineages within the genus

Acinetobacter

was obtained from comparative analysis of the partial sequences of the 16S rRNA gene and the gene encoding the β-subunit of RNA polymerase (rpoB), DNA–DNA reassociation data, determination of the DNA G+C content and physiological tests. The names Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov. are proposed. The type strain of A. nectaris sp. nov. is SAP 763.2T ( = LMG 26958T = CECT 8127T) and that of A. boissieri sp. nov. is SAP 284.1T ( = LMG 26959T = CECT 8128T).
Pseudofulvibacter geojedonensis gen. nov., sp. nov., a polysaccharide-degrading member of the family

Flavobacteriaceae

isolated from seawater, and emended description of the genus

Fulvibacter
Authors: Yoon Jung-Hoon , Lee Mi-Hwa , Jung Yong-Taek
Published: August 2012

A Gram-negative, non-spore-forming, aerobic, non-flagellated, non-gliding rod, designated YCS-9T, was isolated from seawater in the South Sea, South Korea. Strain YCS-9T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain YCS-9T fell within the family

Flavobacteriaceae

and formed a cluster with

Fulvibacter tottoriensis

MTT-39T with a bootstrap resampling value of 75.4 %. Strain YCS-9T showed 92.3 % 16S rRNA gene sequence similarity to

F. tottoriensis

MTT-39T and 89.0–93.7 % sequence similarity to the other strains used in the phylogenetic analysis. Strain YCS-9T contained MK-6 as the only menaquinone and iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 34.2 mol%. Strain YCS-9T could be differentiated from

F. tottoriensis

NBRC 102624T by differences in fatty acid composition, polar lipid profile and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YCS-9T represents a novel species in a new genus within the phylum

Bacteroidetes

, for which the name Pseudofulvibacter geojedonensis gen. nov., sp. nov. is proposed. The type strain of Pseudofulvibacter geojedonensis is YCS-9T ( = KCTC 23884T  = CCUG 62114T). An emended description of the genus

Fulvibacter

is also presented.
Sunxiuqinia faeciviva sp. nov., a facultatively anaerobic organoheterotroph of the

Bacteroidetes

isolated from deep subseafloor sediment
Authors: Takai Ken , Abe Mariko , Miyazaki Masayuki , Koide Osamu , Nunoura Takuro , Imachi Hiroyuki , Inagaki Fumio , Kobayashi Tohru
Published: August 2012

A facultatively anaerobic organoheterotroph, designated JAM-BA0302T, was isolated from a deep subseafloor sediment at a depth of 247.1 m below the seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001 , water depth 1180 m). Cells of strain JAM-BA0302T showed gliding motility and were thin, long rods with peritrichous fimbriae-like structures. Growth occurred at 4–37 °C (optimum 30 °C; doubling time 8 h), at pH 5.4–8.3 (optimum pH 7.5) and with 5–60 g NaCl l−1 (optimum 20–25 g l−1). The isolate utilized proteinaceous substrates such as yeast extract, tryptone, casein and Casamino acids with O2 respiration or fermentation. Strain JAM-BA0302T was a piezotolerant bacterium that could grow at pressures as high as 25 MPa under aerobic conditions and 10 MPa under anaerobic conditions. The G+C content of the genomic DNA was 43.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAM-BA0302T was most closely related to yet-undescribed strains recently isolated from various marine sedimentary environments (>99.6 % 16S rRNA gene sequence similarity) and was moderately related to

Sunxiuqinia elliptica

DQHS-4T, isolated from a sea cucumber farm sediment (95.5 % 16S rRNA gene sequence similarity) within the

Bacteroidetes

. The phylogenetic analysis suggested that the isolate should belong to the genus

Sunxiuqinia

. However, low DNA–DNA relatedness (<11 %) and many physiological and molecular properties differentiated the isolate from those previously described. We propose here a novel species of the genus

Sunxiuqinia

, with the name Sunxiuqinia faeciviva sp. nov. The type strain is JAM-BA0302T ( = JCM 15547T  = NCIMB 14481T).
Olleya namhaensis sp. nov., isolated from wood falls, and emended description of the genus

Olleya

Mancuso Nichols et al. 2005 emend. Lee et al. 2010
Authors: Lee Mi-Hwa , Jung Yong-Taek , Park Sooyeon , Yoon Jung-Hoon
Published: August 2012

A Gram-stain-negative, non-flagellated, gliding, rod-shaped bacterial strain, designated WT-MY15T, was isolated from wood falls in the South Sea in Korea and subjected to a polyphasic taxonomic study. Strain WT-MY15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MY15T clustered with the type strains of two

Olleya

species, exhibiting 16S rRNA gene sequence similarity values of 97.7–98.1 %. Strain WT-MY15T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain WT-MY15T were similar to those of

Olleya aquimaris

L-4T and

Olleya marilimosa

CIP 108537T. The DNA G+C content of strain WT-MY15T was 42.8 mol% and its mean DNA–DNA relatedness values with

O. aquimaris

L-4T and

O. marilimosa

CIP 108537T were 8.3 and 5.6 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MY15T is separate from the two recognized species of the genus

Olleya

. On the basis of the data presented, strain WT-MY15T is considered to represent a novel species of the genus

Olleya

, for which the name Olleya namhaensis sp. nov. is proposed. The type strain is WT-MY15T ( = KCTC 23673T = CCUG 61507T). An emended description of the genus

Olleya

is also presented.
Dyadobacter arcticus sp. nov., isolated from Arctic soil
Authors: Chen Lu , Jiang Fan , Xiao Mengchen , Dai Jun , Kan Wenjing , Fang Chengxiang , Peng Fang
Published: August 2012

A psychrotolerant, Gram-negative, rod-shaped, yellow-pigmented bacterium, designated strain R-S7-29T, was isolated from a soil sample collected from the Svalbard Archipelago in Norway (78° N). Cells were non-motile, aerobic, and catalase- and oxidase-positive. Growth occurred at 4–28 °C (optimum, 18 °C). A phylogenetic tree based on 16S rRNA gene sequences showed that strain R-S7-29T belongs to the genus

Dyadobacter

(family ‘

Flexibacteraceae

’) with sequence similarity to related members of the genus ranging from 95.2 to 96.7 %. The major fatty acids were C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and the predominant respiratory quinone was MK-7. The DNA G+C content of strain R-S7-29T was 50 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic properties, strain R-S7-29T represents a novel species of the genus

Dyadobacter

, for which the name Dyadobacter arcticus sp. nov. is proposed. The type strain is R-S7-29T ( = CCTCC AB 2011022T = NRRL B-59659T).
Fulvitalea axinellae gen. nov., sp. nov., a member of the family Flammeovirgaceae isolated from the Mediterranean sponge Axinella verrucosa
Authors: Haber Markus , Shefer Sigal , Giordano Assunta , Orlando Pierangelo , Gambacorta Agata , Ilan Micha
Published: August 2012

The yellow-pigmented, non-motile, Gram-negative, strictly aerobic, rod-shaped bacterial strain VI.18Twas isolated from the Mediterranean spongeAxinella verrucosacollected off the coast near Sdot Yam, Israel. Results from 16S rRNA gene sequence analysis indicated that the isolate belonged to the familyFlammeovirgaceae. The highest nucleotide similarity (91.4 %) occurred withAureibacter tunicatorumA5Q-118T. The predominant cellular fatty acids of strain VI.18Twere iso-C15 : 0(56.0 %), iso-C17 : 1ω9c(22.8 %) and C16 : 0(7.4 %) and its major respiratory quinone was MK-7. The DNA G+C content was 47.5 mol%. The strain could readily be distinguished from its phylogenetically closest relatives by phenotypic, physiological and chemotaxonomic properties. On the basis of the data from the present polyphasic study, we propose a novel genus and species within the familyFlammeovirgaceae, with the nameFulvitalea axinellaegen. nov., sp. nov. Strain VI.18T( = ATCC BAA-2395T = LMG 26722T) is the type strain ofFulvitalea axinellae.
Algoriphagus zhangzhouensis sp. nov., isolated from mangrove sediment
Authors: Yang Caiyun , Li Yi , Guo Qian , Lai Qiliang , Zheng Tianling , Tian Yun
Published: August 2012

A Gram-negative, short-rod-shaped and non-motile bacterium, strain 12C11T, was isolated from an oil-degrading consortium, enriched from the Fugong mangrove sediment, Fujian Province of China. Optimum growth was observed at 25 °C, at pH 7.5 and with 4 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis demonstrated that it shared highest similarity with members of the genus

Algoriphagus

(97.5–93.4 %), exhibiting 97.5 % sequence similarity to

Algoriphagus ornithinivorans

IMSNU 14014T, followed by

Algoriphagus vanfongensis

KMM 6241T (97.2 %); it shared <96.0 % sequence similarity with other members of the genus. Levels of nucleotide sequence similarity between gyrB (DNA gyrase subunit B) genes of strain 12C11T and

A. vanfongensis

KMM 6241T,

A. ornithinivorans

IMSNU 14014T,

Algoriphagus marincola

SW-2T and

Algoriphagus hitonicola

7-UAHT were 78.8, 78.6, 75.6 and 77.4 %, respectively. Phylogenetic trees based on these housekeeping genes showed that strain 12C11T and other

Algoriphagus

strains formed a distinct lineage. The dominant fatty acids were iso-C15 : 0 (32.1 %), C16 : 1ω7c/C16 : 1ω6c (11.6 %), iso-C17 : 1 I/anteiso-C17 : 1 B (10.1 %), iso-C17 : 0 3-OH (9.2 %) and iso-C17 : 1ω9c/C16 : 0 10-methyl (7.1 %), which accounted for 70.0 % of the total fatty acids. DNA–DNA hybridization showed that strain 12C11T shared low DNA–DNA relatedness with

A. vanfongensis

KMM 6241T and

A. ornithinivorans

IMSNU 14014T (30.7±0.9 and 30.5±1.8 %, respectively). The G+C content of the chromosomal DNA of strain 12C11T was 38.4 mol%. The major respiratory quinones were MK-7 (96.0 %) and MK-6 (4.0 %). According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, the novel strain most appropriately belongs to the genus

Algoriphagus

, but can readily be distinguished from known

Algoriphagus

species. The name Algoriphagus zhangzhouensis sp. nov. is proposed (type strain 12C11T = CGMCC 1.11027T = MCCC 1F01099T = DSM 25035T).
Hirschia litorea sp. nov., isolated from seashore sediment, and emended description of the genus

Hirschia
Authors: Park Sooyeon , Yoon Jung-Hoon
Published: August 2012

A Gram-negative, non-spore-forming, non-flagellated, coccoid-, oval- or rod-shaped strain, designated M-M23T, was isolated from seashore sediment at Geoje island, South Korea. Strain M-M23T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M23T clustered with the type strains of the two species of the genus

Hirschia

, with which it exhibited 97.6–98.1 % 16S rRNA gene sequence similarity. Sequence similarity with the type strains of other recognized species was <90.8 %. Strain M-M23T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain M-M23T were phosphatidylglycerol and two unidentified lipids. The DNA G+C content of strain M-M23T was 45.4 mol%. DNA–DNA relatedness between the isolate and

Hirschia baltica

DSM 5838T and

Hirschia maritima

JCM 14974T was 22±7.2 and 14±5.6 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain M-M23T is separate from the other described members of the genus

Hirschia

. On the basis of the data presented, strain M-M23T is considered to represent a novel species of the genus

Hirschia

, for which the name Hirschia litorea sp. nov. is proposed. The type strain is M-M23T ( = KCTC 32081T  = CCUG 62793T). An emended description of the genus Hirschia is also provided.