bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of very-large-scale motions of turbulent pipe and boundary layer simulations
Authors: Lee Jae Hwa , Sung Hyung Jin
Published: April 2013

A direct numerical simulation of a fully developed turbulent pipe flow was performed to investigate the similarities and differences of very-large-scale motions (VLSMs) to those of turbulent boundary layer (TBL) flows. The Reynolds number was set to ReD = 35 000, and the computational domain was 30 pipe radii in length. Inspection of instantaneous fields, streamwise two-point correlations, and population trends of the momentum regions showed that the streamwise length of the structures in the pipe flow grew continuously beyond the log layer (y/δ < 0.3–0.4) with a large population of long structures (>3δ), and the maximum length of the VLSMs increased up to ∼30δ. Such differences between the TBL and pipe flows arose due to the entrainment of large plumes of the intermittent potential flow in the TBL, creating break-down of the streamwise coherence of the structures above the log layer with the strong swirling strength and Reynolds shear stress. The average streamwise length scale of the pipe flow was approximately 1.5–3.0 times larger than that of the TBL through the log and wake regions. The maximum contribution of the structures to the Reynolds shear stress was observed at approximately 6δ in length, whereas that of the TBL was at 1δ–2δ, indicating a higher contribution of the VLSMs to the Reynolds shear stress in the pipe flow than in the TBL flow.
Design and implementation of a 150 GHz single-channel millimeter wave interferometer on Joint TEXT tokamak
Authors: Feng X. D. , Zhuang G. , Yang Z. J. , Gao L. , Hu X. W.
Published: April 2013

A simple, single-channel millimeter-wave interferometer system has been designed, fabricated, and installed on the J-TEXT tokamak. For the plasma density anticipated on J-TEXT, a solid-state source operating at 150 GHz has been chosen to minimize errors due to both vibration along the beam path and refraction in the plasma. The new aspect of the interferometer design is to use a subharmonic mixer for detection with a frequency doubled 150 GHz source. It employs a single source which is bias-tuned and modulated with a sawtooth wave form up to 100 kHz in order to generate the intermediate frequency. The 12.5 GHz voltage-controlled oscillator is multiplied to 75 GHz before a final doubler raises it to 150 GHz. A portion of the 75 GHZ power is used for the local oscillator (LO) and is directly connected to the LO input of the subharmonic mixer. The phase is evaluated by a digital phase comparator using a software-based algorithm. Detection noise limits the minimum resolvable phase change with the interferometer to ±0.05 fringe, which corresponds to an averaged electron density change along the chord of ±1.1 × 1017 m−2. The maximum measurable electron density is expected to be ∼9 × 1019 m−3. A comparison of preliminary results from the millimeter wave interferometer with that from the far-infrared hydrogen cyanide laser (wavelength of 337 μm) interferometer shows good agreement during the pulse flat-top period. The millimeter wave interferometer system will be used as a part of the density feedback control system in the future.
Dynamics of exciton dissociation in donor-acceptor polymer heterojunctions
Authors: Sun Zhen , Stafström Sven
Published: April 2013

Exciton dissociation in a donor-accepter polymer heterojunction has been simulated using a nonadiabatic molecular dynamics approach, which allows for the coupled evolution of the nuclear degrees of freedom and the electronic degrees of freedom described by multiconfigurational electronic wavefunctions. The simulations reveal important details of the charge separation process: the exciton in the donor polymer first dissociates into a “hot” charge transfer state, which is best described as a polaron pair. The polaron pair can be separated into free polaron charge carriers if a sufficiently strong external electric field is applied. We have also studied the effects of inter-chain interaction, temperature, and the external electric field strength. Increasing inter-chain interactions makes it easier for the exciton to dissociate into a polaron pair state, but more difficult for the polaron pair to dissociate into free charge carriers. Higher temperature and higher electric field strength both favor exciton dissociation as well as the formation of free charge carriers.
Nogo-A is a negative regulator of CNS angiogenesis
Authors: Wälchli Thomas , Pernet Vincent , Weinmann Oliver , Shiu Jau-Ye , Guzik-Kornacka Anna , Decrey Guillaume , Yüksel Deniz , Schneider Hannah , Vogel Johannes , Ingber Donald E. , Vogel Viola , Frei Karl , Schwab Martin E.
Published: April 2013

Nogo-A is an important axonal growth inhibitor in the adult and developing CNS. In vitro, Nogo-A has been shown to inhibit migration and cell spreading of neuronal and nonneuronal cell types. Here, we studied in vivo and in vitro effects of Nogo-A on vascular endothelial cells during angiogenesis of the early postnatal brain and retina in which Nogo-A is expressed by many types of neurons. Genetic ablation or virus-mediated knock down of Nogo-A or neutralization of Nogo-A with an antibody caused a marked increase in the blood vessel density in vivo. In culture, Nogo-A inhibited spreading, migration, and sprouting of primary brain microvascular endothelial cells (MVECs) in a dose-dependent manner and induced the retraction of MVEC lamellipodia and filopodia. Mechanistically, we show that only the Nogo-A–specific Delta 20 domain exerts inhibitory effects on MVECs, but the Nogo-66 fragment, an inhibitory domain common to Nogo-A, -B, and -C, does not. Furthermore, the action of Nogo-A Delta 20 on MVECs required the intracellular activation of the Ras homolog gene family, member A (Rho-A)-associated, coiled-coil containing protein kinase (ROCK)-Myosin II pathway. The inhibitory effects of early postnatal brain membranes or cultured neurons on MVECs were relieved significantly by anti–Nogo-A antibodies. These findings identify Nogo-A as an important negative regulator of developmental angiogenesis in the CNS. They may have important implications in CNS pathologies involving angiogenesis such as stroke, brain tumors, and retinopathies.
On Ramanujan’s definition of mock theta function
Authors: Rhoades Robert C.
Published: April 2013

In his famous “deathbed” letter, Ramanujan “defined” the notion of a mock theta function and offered some examples of functions he believed satisfied his definition. Very recently, Griffin et al. established for the first time that Ramanujan’s mock theta functions actually satisfy his own definition. On the other hand, Zwegers’ 2002 doctoral thesis [Zwegers S (2002) Mock theta functions. PhD thesis (Univ Utrecht, Utrecht, The Netherlands)] showed that all of Ramanujan’s examples are holomorphic parts of harmonic Maass forms. This has led to an alternate definition of a mock theta function. This paper shows that Ramanujan’s definition of mock theta function is not equivalent to the modern definition.
Latency of Epstein–Barr virus is disrupted by gain-of-function mutant cellular AP-1 proteins that preferentially bind methylated DNA
Authors: Yu Kuan-Ping , Heston Lee , Park Richard , Ding Zhaowei , Wang’ondu Ruth , Delecluse Henri-Jacques , Miller George
Published: April 2013

ZEBReplication Activator (ZEBRA), a viral basic zipper protein that initiates the Epstein–Barr viral lytic cycle, binds to DNA and activates transcription through heptamer ZEBRA response elements (ZREs) related to AP-1 sites. A component of the biologic action of ZEBRA is attributable to binding methylated CpGs in ZREs present in the promoters of viral lytic cycle genes. Residue S186 of ZEBRA, Z(S186), which is absolutely required for disruption of latency, participates in the recognition of methylated DNA. We find that mutant cellular AP-1 proteins, Jun(A266S) and Fos(A151S), with alanine-to-serine substitutions homologous to Z(S186), exhibit altered DNA-binding affinity and preferentially bind methylated ZREs. These mutant AP-1 proteins acquire functions of ZEBRA; they activate expression of many viral early lytic cycle gene transcripts in cells harboring latent EBV but are selectively defective in activating expression of some viral proteins and are unable to promote viral DNA replication. Transcriptional activation by mutant c-Jun and c-Fos that have acquired the capacity to bind methylated CpG challenges the paradigm that DNA methylation represses gene expression.
A cinematographic analysis of Palestinian recording films: moving in a damaged space, surrounded by moral and material walls!
Authors: Farhat Mohammad Na’im
Published: April 2013

This study deals with a number of recording films produced by Palestinian women living under the Israeli occupation. As for their main issue, the films are about awareness as depicted by these women. The study focuses on reading the recordings as one text comprised of various parts pertaining to numerous viewpoints regarding a reality, the characteristics of which have got much in common in terms of depth and comprehensiveness. Therefore, this study is auxiliary in exploring and highlighting the basic signs which these films present. This trend puts the study, from a theoretical and methodological viewpoint, together, directly and indirectly, within a context of rich heritage, i.e. the sociology of culture, extending from Lucien Goldman to many others, on the basis that this context is the most appropriate for such studies. This also explains its recourse to a number of basic concepts centred on world vision, text, discourse, semiotics and awareness.
KGVDB: a population-based genomic map of CNVs tagged by SNPs in Koreans
Authors: Moon Sanghoon , Jung Kwang Su , Kim Young Jin , Hwang Mi Yeong , Han Kyungsook , Lee Jong-Young , Park Kiejung , Kim Bong-Jo
Published: April 2013

Summary: Despite a growing interest in a correlation between copy number variations (CNVs) and flanking single nucleotide polymorphisms, few databases provide such information. In particular, most information on CNV available so far was obtained in Caucasian and Yoruba populations, and little is known about CNV in Asian populations. This article presents a database that provides CNV regions tagged by single nucleotide polymorphisms in about 4700 Koreans, which were detected under strict quality control, manually curated and experimentally validated.

Availability: KGVDB is freely available for non-commercial use at http://biomi.cdc.go.kr/KGVDB.

Contact:  kbj6181@cdc.go.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
OCSANA: optimal combinations of interventions from network analysis
Authors: Vera-Licona Paola , Bonnet Eric , Barillot Emmanuel , Zinovyev Andrei
Published: April 2013

Targeted therapies interfering with specifically one protein activity are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins in signaling networks involved in the disease is often necessary. Thus, one important problem in biomedical research is the design and prioritization of optimal combinations of interventions to repress a pathological behavior, while minimizing side-effects. OCSANA (optimal combinations of interventions from network analysis) is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes. When specified by the user, OCSANA seeks to additionally minimize the side effects that a combination of interventions can cause on specified off-target nodes. With the crucial ability to cope with very large networks, OCSANA includes an exact solution and a novel selective enumeration approach for the combinatorial interventions’ problem.

Availability: The latest version of OCSANA, implemented as a plugin for Cytoscape and distributed under LGPL license, is available together with source code at http://bioinfo.curie.fr/projects/ocsana.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  paola.vera-licona@curie.fr
Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites
Authors: Chen Xiang , Qiu Jian-Ding , Shi Shao-Ping , Suo Sheng-Bao , Huang Shu-Yun , Liang Ru-Ping
Published: April 2013

Motivation: Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because of the significant roles ubiquitylation play not only in protein degradation but also in many other cellular functions. High-throughput experimental studies using mass spectrometry have identified many ubiquitylation sites, primarily from eukaryotes. However, the vast majority of ubiquitylation sites remain undiscovered, even in well-studied systems. Because mass spectrometry–based experimental approaches for identifying ubiquitylation events are costly, time-consuming and biased toward abundant proteins and proteotypic peptides, in silico prediction of ubiquitylation sites is a potentially useful alternative strategy for whole proteome annotation. Because of various limitations, current ubiquitylation site prediction tools were not well designed to comprehensively assess proteomes.

Results: We present a novel tool known as UbiProber, specifically designed for large-scale predictions of both general and species-specific ubiquitylation sites. We collected proteomics data for ubiquitylation from multiple species from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates the information from key positions and key amino acid residues. Cross-validation tests reveal that UbiProber achieves some improvement over existing tools in predicting species-specific ubiquitylation sites. Moreover, independent tests show that UbiProber improves the areas under receiver operating characteristic curves by ∼15% by using the Combined model.

Availability: The UbiProber server is freely available on the web at http://bioinfo.ncu.edu.cn/UbiProber.aspx. The software system of UbiProber can be downloaded at the same site.

Contact:  jdqiu@ncu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
NetworkTrail—a web service for identifying and visualizing deregulated subnetworks
Authors: Stöckel Daniel , Müller Oliver , Kehl Tim , Gerasch Andreas , Backes Christina , Rurainski Alexander , Keller Andreas , Kaufmann Michael , Lenhof Hans-Peter
Published: April 2013

Summary: The deregulation of biochemical pathways plays a central role in many diseases like cancer or Parkinsons’s disease. In silico tools for calculating these deregulated pathways may help to gain new insights into pathogenic mechanisms and may open novel avenues for therapy stratification in the sense of personalized medicine. Here, we present NetworkTrail, a web service for the detection of deregulated pathways and subgraphs in biological networks. NetworkTrail uses a state-of-the-art integer linear programming-based approach for this task and offers interfaces to the Biological Network Analyzer (BiNA) and Cytoscape Web for visualizing the resulting subnetworks. By providing an accessible interface to otherwise hard-to-use command line tools, the new web service enables non-experts to quickly and reliably carry out this type of network analyses.

Availability and implementation: NetworkTrail is a JavaServer Pages-based web service. The algorithm for finding deregulated subnetworks has been implemented in C++. NetworkTrail is available at http://networktrail.bioinf.uni-sb.de/.

Contact: dstoeckel@bioinf.uni-sb.de
Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the

Deferribacteraceae
Authors: Rauschenbach Ines , Posternak Valeriya , Cantarella Pasquale , McConnell Jennifer , Starovoytov Valentin , Häggblom Max M.
Published: April 2013

A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4T also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4T is a novel member of the family

Deferribacteraceae

, with the type strain of

Denitrovibrio acetiphilus

as its closest cultivated relative, with 91.5 % sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14 : 0, C15 : 0, C16 : 0, C17 : 0 and C18 : 0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4T represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4T ( = DSM 24984T = ATCC BAA-2290T).
Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces
Authors: Takada Toshihiko , Kurakawa Takashi , Tsuji Hirokazu , Nomoto Koji
Published: April 2013

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11T, KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99 % sequence similarity) and represented a previously unknown subline within the

Blautia coccoides

rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11T were

Clostridium bolteae

WAL 16351T (93.7 % 16S rRNA gene sequence similarity) and

Clostridium saccharolyticum

WM1T (93.7 % similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16 : 0, C18 : 1ω7c DMA and C16 : 0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9–47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11T, KO-38 and TT-111 represent a novel species in a new genus of the family

Lachnospiraceae

, for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11T ( = YIT 12554T = JCM 18507T = DSM 26062T).
Oceanobacillus

chungangensis sp. nov., isolated from a sand dune
Authors: Lee Dong Chae , Kang Hyeonji , Weerawongwiwat Veeraya , Kim Beomjoon , Choi Young-Wan , Kim Wonyong
Published: April 2013

A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterial strain, designated CAU 1051T, was isolated from a sand dune and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1051T grew optimally at pH 5.0 and 30 °C. NaCl was not required for growth but up to 10.0 % (w/v) NaCl was tolerated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1051T formed a distinct lineage within the genus

Oceanobacillus

and was most closely related to

Oceanobacillus profundus

CL-MP28T,

Oceanobacillus caeni

S-11T, and

Oceanobacillus picturae

LMG 19492T (96.8 %, 95.6 % and 95.3 % similarity, respectively). DNA–DNA reassociation analysis showed that strain CAU 1051T displayed 28.2±0.7 % relatedness to

O. profundus

KCTC 13625T. Strain CAU 1051T contained MK-7 as the only isoprenoid quinone and anteiso-C15 : 0 as the major fatty acid. The cell wall peptidoglycan of strain CAU 1051T contained meso-diaminopimelic acid. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, six unidentified phospholipids, an unidentified glycolipid, and six unidentified polar lipids. The major whole-cell sugars were glucose and ribose. The DNA G+C content was 36.3 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1051T represents a novel species of the genus

Oceanobacillus

for which the name

Oceanobacillus

chungangensis sp. nov. is proposed. The type strain is CAU 1051T ( = KCTC 33035T = CCUG 63270T).
Gillisia marina sp. nov., from seashore sand, and emended description of the genus

Gillisia
Authors: Roh Seong Woon , Lee Myunglip , Lee Hae-Won , Yim Kyung June , Heo Soo Yeon , Kim Kil-Nam , Yoon Changmann , Nam Young-Do , Kim Joon Yong , Hyun Dong-Wook , Bae Jin-Woo , Jeong Joon Bum , Kang Heewan , Kim Daekyung
Published: April 2013

A Gram-staining-negative, strictly aerobic, rod-shaped bacterium, designated CBA3202T, was isolated from seashore sand on Jeju Island, Republic of Korea. Based on the 16S rRNA gene sequence analysis, strain CBA3202T was allocated to the genus

Gillisia

(family

Flavobacteriaceae

) and was most closely related to the type strain of

Gillisia mitskevichiae

(99.0 % 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C and with 3 % NaCl. The only isoprenoid quinone was menaquinone-6 (MK-6), the predominant fatty acids were C16 : 0, iso-C15 : 1 G, iso-C16 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), and the DNA G+C content was 34.9 mol%. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids and several unidentified polar lipids. Based on phylogenetic inference and phenotypic data, we conclude that strain CBA3202T represents a novel species of the genus

Gillisia

, for which the name Gillisia marina sp. nov. is proposed. The type strain is CBA3202T ( = KACC 16693T = KCTC 32030T = JCM 18402T). An emended description of the genus

Gillisia

is also provided.
Bacillus

thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus
Authors: Yang Guiqin , Zhou Xuemei , Zhou Shungui , Yang Dehui , Wang Yueqiang , Wang Dingmei
Published: April 2013

A novel thermotolerant bacterium, designated SgZ-8T, was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20–65 °C (optimum 50 °C) and pH 6.0–9.0 (optimum 6.5–7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6-disulphonate (AQDS), fumarate and NO3
- as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8T into the genus

Bacillus

, with the highest similarity to

Bacillus badius

JCM 12228T (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus

Bacillus

. The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8T ( = CCTCC AB 2012108T = KACC 16706T) was designated the type strain of a novel species of the genus

Bacillus

, for which the name

Bacillus

thermotolerans sp. nov. is proposed.
Algibacter

undariae sp. nov., isolated from a brown algae reservoir
Authors: Park Sooyeon , Lee Jung-Sook , Lee Keun-chul , Yoon Jung-Hoon
Published: April 2013

A Gram-stain-negative, non-flagellated, rod-shaped bacterial strain able to move by gliding, designated WS-MY9T, was isolated from a brown algae reservoir in South Korea. Strain WS-MY9T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WS-MY9T clustered with the type strain of

Algibacter lectus

with a bootstrap resampling value of 100 %. Strain WS-MY9T exhibited 16S rRNA gene sequence similarity values of 98.5 and 96.7 % to the type strains of

A. lectus

and

Algibacter mikhailovii

, respectively, and less than 96.1 % sequence similarity to other members of the family

Flavobacteriaceae

. Strain WS-MY9T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 as the major fatty acids. The major polar lipids of strain WS-MY9T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain WS-MY9T was 35.0 mol% and its DNA–DNA relatedness value with

A. lectus

KCTC 12103T was 15 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WS-MY9T is separate from the two recognized species of the genus

Algibacter

. On the basis of the data presented, strain WS-MY9T represents a novel species of the genus

Algibacter

, for which the name

Algibacter

undariae sp. nov. is proposed. The type strain is WS-MY9T ( = KCTC 32259T = CCUG 63684T).
Paenibacillus

taihuensis sp. nov., isolated from an eutrophic lake
Authors: Wu Yu-Fan , Wu Qing-Long , Liu Shuang-Jiang
Published: April 2013

Two Gram-stain-negative, facultatively anaerobic and endospore-forming rod-shaped bacterial strains, THMBG22T and R24, were isolated from decomposing algal scum. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to each other (99.7 % similarity) and that they were also closely related to

Paenibacillus sacheonensis

DSM 23054T (97–97.1 %) and
Paenibacillus phyllosphaerae
DSM 17399T (96.1–96.4 %). This affiliation was also supported by rpoB-based phylogenetic analyses. Growth was observed at 20–40 °C (optimum, 30–37 °C) and at pH 5.0–9.0 (optimum, pH 6.0–7.0). The cells contained MK-7 as the sole respiratory quinone and anteiso-C15 : 0 as the major cellular fatty acid. Their cellular polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and 12 unidentified polar lipids. The diamino acid of their cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA–DNA hybridization value between THMBG22T and R24 was 84 %, and DNA–DNA relatedness to the most closely related species with a validly published name (

P. sacheonensis

) was 35–37 %. These results supported the assignment of the new isolates to the genus

Paenibacillus

and also distinguished them from the previously described species of the genus

Paenibacillus

. Hence, it is proposed that strains THMBG22T and R24 represent a novel species of the genus

Paenibacillus

, with the name

Paenibacillus

taihuensis sp. nov. The type strain is THMBG22T ( = CGMCC 1.10966T = NBRC 108766T).
Sugiyamaella xylanicola sp. nov., a xylan-degrading yeast species isolated from rotting wood
Authors: Morais Camila G. , Lara Carla A. , Marques Susana , Fonseca Cesar , Lachance Marc-André , Rosa Carlos A.
Published: April 2013

Four strains of a novel yeast species were isolated from rotting-wood samples in an Atlantic rainforest site in the state of Minas Gerais, Brazil. These yeasts were obtained from enrichments using yeast nitrogen base (YNB)-d-xylose or YNB-xylan media. The novel yeast species produces bacilliform ascospores typical of the genus Sugiyamaella, and its closest described relative in terms of sequence similarity is Candida (iter. nom. Sugiyamaella) marionensis. The yeast is able to grow in medium with xylan as sole carbon source and produces extracellular enzymes with xylanolytic activities. The novel species Sugiyamaella xylanicola sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-CA-32.1T ( = CBS 12683T  = CBMAI 1467T).
Tetrapisispora taiwanensis sp. nov. and Tetrapisispora pingtungensis sp. nov., two ascosporogenous yeast species isolated from soil
Authors: Chen Shan-Fu , Lo Shih Feng , Chang Chin-Feng , Lee Ching-Fu
Published: April 2013

Two novel yeast species, Tetrapisispora taiwanensis sp. nov. and Tetrapisispora pingtungensis sp. nov., belonging to the Saccharomycetaceae within the Saccharomycetales, are proposed to accommodate six strains isolated from samples of Taiwanese forest soil between 2005 and 2010. Sequence analysis of the internal transcribed spacer (ITS) and the D1/D2 domains of the large-subunit (LSU) rRNA gene revealed that the two species are phylogenetically closely related to species of the genus Tetrapisispora. Moreover, the assimilation spectrum of carbon and nitrogen sources and morphological characteristics are very similar to those of other Tetrapisispora species. The molecular, morphological and physiological characteristics described above indicate that these two species should be classified as members of the genus Tetrapisispora. The two species can be differentiated from each other and from other Tetrapisispora species based on their LSU D1/D2 rRNA gene and ITS sequences. Thus, the two species could be regarded as novel species of the genus Tetrapisispora, and the names Tetrapisispora taiwanensis sp. nov. (type strain SJ6S04T  = CBS 10586T  = NBRC 102652T  = BCRC 23090T) and Tetrapisispora pingtungensis sp. nov. (type strain NC2S06T  = CBS 12780T  = BCRC 23409T) are proposed. The type strains of the two species were isolated from forest soil in Leinhuatsu Park, Nantou, in 2006 and from Hungchun, Pingtung, in 2009, respectively.
Fabibacter

pacificus sp. nov., a moderately halophilic bacterium isolated from seawater
Authors: Huo Ying-Yi , Xu Lin , Wang Chun-Sheng , Yang Jun-Yi , You Hong , Oren Aharon , Xu Xue-Wei
Published: April 2013

A Gram-stain-negative, aerobic, moderately halophilic bacterium, strain DY53T, was isolated from a deep-seawater sample collected from the eastern Pacific Ocean. This isolate grew in the presence of 0.5–10.0 % (w/v) NaCl, at pH 6.5–8.5 and at 15–40 °C. The optimum NaCl concentration for growth of DY53T was 2 % (w/v) at 35 °C. Chemotaxonomic analysis showed MK-7 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH as major cellular fatty acids. The genomic DNA G+C content was 40.8 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that

Fabibacter halotolerans

UST030701-097T was the closest neighbour, with 96.7 % sequence similarity. Based on phylogenetic, chemotaxonomic and phenotypic data, we propose that strain DY53T represents a novel species of the genus

Fabibacter

, for which the name

Fabibacter

pacificus sp. nov. is proposed. The type strain is DY53T( = CGMCC 1.12402T = JCM 18885T).
Janibacter

cremeus sp. nov., an actinobacterium isolated from sea sediment
Authors: Hamada Moriyuki , Shibata Chiyo , Tamura Tomohiko , Yamamura Hideki , Hayakawa Masayuki , Suzuki Ken-ichiro
Published: April 2013

A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus

Janibacter

, with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus

Janibacter

. Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus

Janibacter

. Therefore, strain HR08-44T represents a novel species of the genus

Janibacter

, for which the name

Janibacter

cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).
Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field
Authors: Honda Takuya , Fujita Takashi , Tonouchi Akio
Published: April 2013

A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6ET, were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0–2.5 µm) with two or three lateral flagella. Growth occurred at 20–42 °C (optimum at 37–40 °C), at pH 6.4–8.4 (optimum at pH 7.3) and at 0–1.5 % (w/v) NaCl (optimum at 0–0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, l-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen

Methanobacterium formicicum

JCM 10132T, strain 4F6ET oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of

Fretibacterium fastidiosum

,

Aminobacterium colombiense

and

Aminobacterium mobile

, members of the family

Synergistaceae

, were the closest relatives of strain 4F6ET, with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6ET contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of

F. fastidiosum

,

Aminobacterium colombiense

and

Aminobacterium mobile

. On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6ET and the type strains of

F. fastidiosum

and

Aminobacterium

species, we propose that strain 4F6ET represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6ET ( = JCM 18417T = DSM 25964T).
Hansschlegelia

beijingensis sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic bacterium isolated from watermelon rhizosphere soil
Authors: Zou Xiao-lin , Li Xiu-ai , Wang Xu-Ming , Chen Qiang , Gao Miao , Qiu Tian-lei , Sun Jian-guang , Gao Jun-lian
Published: April 2013

A novel Gram-stain-negative, aerobic, rod-shaped strain designated PG04T was isolated from the rhizosphere of watermelon plants cultivated in Beijing, China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, isolate PG04T belonged clearly to the genus

Hansschlegelia

and was most closely related to

Hansschlegelia zhihuaiae

(97.3 % similarity to the type strain). The predominant respiratory quinone was ubiquinone 10 (Q-10) and the polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids were C18 : 1ω7c (41.3 %), C19 : 0 cyclo ω8c (30.6 %) and C16 : 0 (19.1 %). The G+C content of the DNA was about 64.4 mol%. DNA–DNA hybridization experiments showed 34.4 % relatedness between strain PG04T and

H. zhihuaiae

DSM 18984T. The results of physiological and biochemical tests and differences in fatty acid profiles allowed clear phenotypic differentiation of strain PG04T from the most closely related species in the genus,

H. zhihuaiae

. Strain PG04T therefore represents a novel species within the genus

Hansschlegelia

, for which the name

Hansschlegelia

beijingensis sp. nov. is proposed, with the type strain PG04T ( = DSM 25481T = ACCC 05759T).
A Basic Helix-Loop-Helix Transcription Factor, PtrbHLH, of Poncirus trifoliata Confers Cold Tolerance and Modulates Peroxidase-Mediated Scavenging of Hydrogen Peroxide
Authors: Huang Xiao-San , Wang Wei , Zhang Qian , Liu Ji-Hong
Published: April 2013

The basic helix-loop-helix (bHLH) transcription factors are involved in a variety of physiological processes. However, plant bHLHs functioning in cold tolerance and the underlying mechanisms remain poorly understood. Here, we report the identification and functional characterization of PtrbHLH isolated from trifoliate orange (Poncirus trifoliata). The transcript levels of PtrbHLH were up-regulated under various abiotic stresses, particularly cold. PtrbHLH was localized in the nucleus with transactivation activity. Overexpression of PtrbHLH in tobacco (Nicotiana tabacum) or lemon (Citrus limon) conferred enhanced tolerance to cold under chilling or freezing temperatures, whereas down-regulation of PtrbHLH in trifoliate orange by RNA interference (RNAi) resulted in elevated cold sensitivity. A range of stress-responsive genes was up-regulated or down-regulated in the transgenic lemon. Of special note, several peroxidase (POD) genes were induced after cold treatment. Compared with the wild type, POD activity was increased in the overexpression plants but decreased in the RNAi plants, which was inversely correlated with the hydrogen peroxide (H2O2) levels in the tested lines. Treatment of the transgenic tobacco plants with POD inhibitors elevated the H2O2 levels and greatly compromised their cold tolerance, while exogenous replenishment of POD enhanced cold tolerance of the RNAi line. In addition, transgenic tobacco and lemon plants were more tolerant to oxidative stresses. Yeast one-hybrid assay and transient expression analysis demonstrated that PtrbHLH could bind to the E-box elements in the promoter region of a POD gene. Taken together, these results demonstrate that PtrbHLH plays an important role in cold tolerance, at least in part, by positively regulating POD-mediated reactive oxygen species removal.
Involvement of the Sieve Element Cytoskeleton in Electrical Responses to Cold Shocks
Authors: Hafke Jens B. , Ehlers Katrin , Föller Jens , Höll Sabina-Roxana , Becker Stefanie , van Bel Aart J.E.
Published: April 2013

This study dealt with the visualization of the sieve element (SE) cytoskeleton and its involvement in electrical responses to local cold shocks, exemplifying the role of the cytoskeleton in Ca2+-triggered signal cascades in SEs. High-affinity fluorescent phalloidin as well as immunocytochemistry using anti-actin antibodies demonstrated a fully developed parietal actin meshwork in SEs. The involvement of the cytoskeleton in electrical responses and forisome conformation changes as indicators of Ca2+ influx was investigated by the application of cold shocks in the presence of diverse actin disruptors (latrunculin A and cytochalasin D). Under control conditions, cold shocks elicited a graded initial voltage transient, ƊV1, reduced by external La3+ in keeping with the involvement of Ca2+ channels, and a second voltage transient, ƊV2. Cytochalasin D had no effect on ƊV1, while ƊV1 was significantly reduced with 500 nm latrunculin A. Forisome dispersion was triggered by cold shocks of 4°C or greater, which was indicative of an all-or-none behavior. Forisome dispersion was suppressed by incubation with latrunculin A. In conclusion, the cytoskeleton controls cold shock-induced Ca2+ influx into SEs, leading to forisome dispersion and sieve plate occlusion in fava bean (Vicia faba).
Reduced Tonoplast Fast-Activating and Slow-Activating Channel Activity Is Essential for Conferring Salinity Tolerance in a Facultative Halophyte, Quinoa
Authors: Bonales-Alatorre Edgar , Shabala Sergey , Chen Zhong-Hua , Pottosin Igor
Published: April 2013

Halophyte species implement a “salt-including” strategy, sequestering significant amounts of Na+ to cell vacuoles. This requires a reduction of passive Na+ leak from the vacuole. In this work, we used quinoa (Chenopodium quinoa) to investigate the ability of halophytes to regulate Na+-permeable slow-activating (SV) and fast-activating (FV) tonoplast channels, linking it with Na+ accumulation in mesophyll cells and salt bladders as well as leaf photosynthetic efficiency under salt stress. Our data indicate that young leaves rely on Na+ exclusion to salt bladders, whereas old ones, possessing far fewer salt bladders, depend almost exclusively on Na+ sequestration to mesophyll vacuoles. Moreover, although old leaves accumulate more Na+, this does not compromise their leaf photochemistry. FV and SV channels are slightly more permeable for K+ than for Na+, and vacuoles in young leaves express less FV current and with a density unchanged in plants subjected to high (400 mm NaCl) salinity. In old leaves, with an intrinsically lower density of the FV current, FV channel density decreases about 2-fold in plants grown under high salinity. In contrast, intrinsic activity of SV channels in vacuoles from young leaves is unchanged under salt stress. In vacuoles of old leaves, however, it is 2- and 7-fold lower in older compared with young leaves in control- and salt-grown plants, respectively. We conclude that the negative control of SV and FV tonoplast channel activity in old leaves reduces Na+ leak, thus enabling efficient sequestration of Na+ to their vacuoles. This enables optimal photosynthetic performance, conferring salinity tolerance in quinoa species.
Elucidation of the Structure and Reaction Mechanism of Sorghum Hydroxycinnamoyltransferase and Its Structural Relationship to Other Coenzyme A-Dependent Transferases and Synthases
Authors: Walker Alexander M. , Hayes Robert P. , Youn Buhyun , Vermerris Wilfred , Sattler Scott E. , Kang ChulHee
Published: April 2013

Hydroxycinnamoyltransferase (HCT) from sorghum (Sorghum bicolor) participates in an early step of the phenylpropanoid pathway, exchanging coenzyme A (CoA) esterified to p-coumaric acid with shikimic or quinic acid as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to elucidate the mode of action of this enzyme, we have determined the crystal structures of SbHCT in its apo-form and ternary complex with shikimate and p-coumaroyl-CoA, which was converted to its product during crystal soaking. The structure revealed the roles of threonine-36, serine-38, tyrosine-40, histidine-162, arginine-371, and threonine-384 in catalysis and specificity. Based on the exact chemistry of p-coumaroyl-CoA and shikimic acid in the active site and an analysis of kinetic and thermodynamic data of the wild type and mutants, we propose a role for histidine-162 and threonine-36 in the catalytic mechanism of HCT. Considering the calorimetric data, substrate binding of SbHCT should occur sequentially, with p-coumaroyl-CoA binding prior to the acyl acceptor molecule. While some HCTs can use both shikimate and quinate as an acyl acceptor, SbHCT displays low activity toward quinate. Comparison of the structure of sorghum HCT with the HCT involved in chlorogenic acid synthesis in coffee (Coffea canephora) revealed many shared features. Taken together, these observations explain how CoA-dependent transferases with similar structural features can participate in different biochemical pathways across species.
Characterization of the Complex Regulation of AtALMT1 Expression in Response to Phytohormones and Other Inducers
Authors: Kobayashi Yasufumi , Kobayashi Yuriko , Sugimoto Miki , Lakshmanan Venkatachalam , Iuchi Satoshi , Kobayashi Masatomo , Bais Harsh P. , Koyama Hiroyuki
Published: April 2013

In Arabidopsis (Arabidopsis thaliana), malate released into the rhizosphere has various roles, such as detoxifying rhizotoxic aluminum (Al) and recruiting beneficial rhizobacteria that induce plant immunity. ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (AtALMT1) is a critical gene in these responses, but its regulatory mechanisms remain unclear. To explore the mechanism of the multiple responses of AtALMT1, we profiled its expression patterns in wild-type plants, in transgenic plants harboring various deleted promoter constructs, and in mutant plants with defects in signal transduction in response to various inducers. AtALMT1 transcription was clearly induced by indole-3-acetic acid (IAA), abscisic acid (ABA), low pH, and hydrogen peroxide, indicating that it was able to respond to multiple signals, while it was not induced by methyl jasmonate and salicylic acid. The IAA-signaling double mutant nonphototropic hypocotyls4-1; auxin-responsive factor19-1 and the ABA-signaling mutant aba insensitive1-1 did not respond to auxin and ABA, respectively, but both showed an Al response comparable to that of the wild type. A synthetic microbe-associated molecular pattern peptide, flagellin22 (flg22), induced AtALMT1 transcription but did not induce the transcription of IAA- and ABA-responsive biomarker genes, indicating that both Al and flg22 responses of AtALMT1 were independent of IAA and ABA signaling. An in planta β-glucuronidase reporter assay identified that the ABA response was regulated by a region upstream (−317 bp) from the first ATG codon, but other stress responses may share critical regulatory element(s) located between −292 and −317 bp. These results illustrate the complex regulation of AtALMT1 expression during the adaptation to abiotic and biotic stresses.
The Arabidopsis B-BOX Protein BBX25 Interacts with HY5, Negatively Regulating BBX22 Expression to Suppress Seedling Photomorphogenesis
Authors: Gangappa Sreeramaiah N. , Crocco Carlos D. , Johansson Henrik , Datta Sourav , Hettiarachchi Chamari , Holm Magnus , Botto Javier F.
Published: April 2013

ELONGATED HYPOCOTYL5 (HY5) is a basic domain/leucine zipper (bZIP) transcription factor, central for the regulation of seedling photomorphogenesis. Here, we identified a B-BOX (BBX)–containing protein, BBX25/SALT TOLERANCE HOMOLOG, as an interacting partner of HY5, which has been previously found to physically interact with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1). BBX25 physically interacts with HY5 both in vitro and in vivo. By physiological and genetic approaches, we showed that BBX25 is a negative regulator of seedling photomorphogenesis. BBX25 and its homolog BBX24 regulate deetiolation processes and hypocotyl shade avoidance response in an additive manner. Moreover, genetic relationships of bbx25 and bbx24 with hy5 and cop1 revealed that BBX25 and BBX24 additively enhance COP1 and suppress HY5 functions. BBX25 accumulates in a light-dependent manner and undergoes COP1-mediated degradation in dark and light conditions. Furthermore, a protoplast cotransfection assay showed that BBX24 and BBX25 repress BBX22 expression by interfering with HY5 transcriptional activity. As HY5 binds to the BBX22 promoter and promotes its expression, our results identify a direct mechanism through which the expression of BBX22 is regulated. We suggest that BBX25 and BBX24 function as transcriptional corepressors, probably by forming inactive heterodimers with HY5, downregulating BBX22 expression for the fine-tuning of light-mediated seedling development.