bluuebunny/crossref_metadata_2025 huggingface dataset:
Fine-tuning in GGM and the 126 GeV Higgs particle
Authors: Lalak Zygmunt , Lewicki Marek
Published: May 2013

Abstract

In this paper we reanalyze the issue of fine-tuning in supersymmetric models which feature Generalized Gauge Mediation (GGM) in the light of recent measurement of the mass of the light Higgs particle and taking into account available data on the value of the muon magnetic moment
$ {g_{\mu }}-2 $
. We consider GGM models with 3, 5 and 6 input parameters and reduce the fine-tuning by assuming simple relations between them at the high scale. We are able to find solutions which give the correct value of the light Higgs mass and are less fine-tuned than models with standard gauge mediation (and with gravity mediation), however one never finds fine-tung measure lower than about 102 if one neglects the data on
$ {g_{\mu }}-2 $
and and about four times more if one takes the constraint given by
$ {g_{\mu }}-2 $
into account. In general the current
$ {g_{\mu }}-2 $
data push the models towards the high fine-tuning region. It is interesting to note, that once one removes the contributions to the finetuning induced by μ and B

μ
, then in the case with neglected
$ {g_{\mu }}-2 $
constraint one can easily find realistic vacua with fine-tuning of order 1 or lower, while the fine-tung remains always large when the
$ {g_{\mu }}-2 $
constraint is enforced. One should note, that in the last case even a small shift of the light Higgs mass towards smaller values both reduces fine-tuning and helps to improve agreement of a model with
$ {g_{\mu }}-2 $
data.
Viscoelastic melt rheology and time–temperature superposition of polycarbonate–multi-walled carbon nanotube nanocomposites
Authors: Choong Gabriel Y. H. , De Focatiis Davide S. A. , Hassell David G.
Published: May 2013

This work investigates the linear and non-linear viscoelastic melt rheology of four grades of polycarbonate melt compounded with 3 wt% Nanocyl NC7000 multi-walled carbon nanotubes and of the matching matrix polymers. Amplitude sweeps reveal an earlier onset of non-linearity and a strain overshoot in the nanocomposites. Mastercurves are constructed from isothermal frequency sweeps using vertical and horizontal shifting. Although all nanocomposites exhibit a second plateau at ∼105Pa, the relaxation times estimated from the peak in loss tangent are not statistically different from those of pure melts estimated from cross-over frequencies: all relaxation timescales scale with molar mass in the same way, evidence that the relaxation of the polymer network is the dominant mechanism in both filled and unfilled materials. Non-linear rheology is also measured in large amplitude oscillatory shear. A comparison of the responses from frequency and amplitude sweep experiments reveals the importance of strain and temperature history on the response of such nanocomposites.
Incidental Findings from Clinical Genome‐Wide Sequencing: A Review
Authors: Lohn Z. , Adam S. , Birch P. H. , Friedman J. M.
Published: May 2013

There are several unresolved challenges associated with the clinical application of genome‐wide sequencing technologies. One of the most discussed issues is incidental findings (IF), which are defined as discoveries made as a result of genetic testing that are unrelated to the indication for the test. The discussion surrounding IF began in the context of research, which we have used to frame consideration of IF in the clinical context. There is growing consensus that analytically valid and medically actionable IF should be offered to patients, but whether and to what extent clinicians should disclose other kinds of IF is debated. While others have systematically reviewed the literature concerning genetic IF, previous reviews focus on ethical and research‐related issues and do not consider the implications for the genetic counseling profession specifically. This review discusses the practical considerations, ethical concerns and genetic counseling issues related to IF, with a particular focus on clinical genome‐wide sequencing. To date, the bulk of the literature with respect to IF in the clinical context consists of commentaries, reviews and case reports. There is a need for more empirical studies to provide a foundation for institutional protocols and evidence‐based clinical practice standards.
Effect of a Hydrophilic Head Group on Krafft Temperature, Surface Activities and Rheological Behaviors of Erucyl Amidobetaines
Authors: Wang Yuejiao , Zhang Yongmin , Liu Xingli , Wang Jiyu , Wei Limin , Feng Yujun
Published: May 2013

Ultra‐long‐chain amidobetaine surfactants have become one of the hot topics recently, but the influence of the hydrophilic head group on the aggregation behaviors and the correlation between surface activities and thickening ability have been less documented. In this work, comparative studies on the effect of the hydrophilic group on Krafft temperature (TK), surface activities and rheological behaviors of erucyl amidobetaines with sulfonate, hydroxyl‐sulfonate or carboxylate were examined. Compared to the sulfobetaines, the carboxybetaine is more water‐soluble; the addition of an hydroxyl group onto the head group of sulfobetaine increases water‐solubility leading to a lower TK. Unexpectedly, the nature of the head groups has little effect on the critical micelle concentration and thickening ability of these surfactants. The packing parameter prediction verifies the formation of wormlike micelles which accounts for the strong thickening ability of the surfactant aqueous solutions.
Effects of Storage Temperature, Atmosphere and Light on Chemical Stability of Astaxanthin Nanodispersions
Authors: Anarjan Navideh , Tan Chin Ping
Published: May 2013

Astaxanthin, as a functional lipid, can be incorporated easily into different water‐based food formulations in the form of a nanodispersion. In this study, astaxanthin nanodispersions were produced using different stabilizer systems, namely, polysorbate 20 (PS20), sodium caseinate (SC), gum arabic (GA) and an optimum combination of these three stabilizers (OPT). Since astaxanthin is sensitive to oxidative damage, its degradations kinetics in the prepared nanodispersion systems were investigated as a function of storage temperature, atmosphere and light. The results showed that astaxanthin degradation followed a first‐order kinetic and, in most cases, astaxanthin was more stable in optimum‐formulated three‐component‐stabilized nanodispersions as compared to nanodispersion systems stabilized by individual stabilizers. In addition, high storage temperature and intense illumination significantly (P < 0.05) increased the degradation of astaxanthin, while oxygen‐free conditions significantly (P < 0.05) reduced the astaxanthin degradation rate.
In vivo mutation of pre‐mRNA processing factor 8 (Prpf8) affects transcript splicing, cell survival and myeloid differentiation
Authors: Keightley Maria-Cristina , Crowhurst Meredith O. , Layton Judith E. , Beilharz Traude , Markmiller Sebastian , Varma Sony , Hogan Benjamin M. , de Jong-Curtain Tanya A. , Heath Joan K. , Lieschke Graham J.
Published: May 2013

Mutated spliceosome components are recurrently being associated with perturbed tissue development and disease pathogenesis. Cephalophŏnus (cph), is a zebrafish mutant carrying an early premature STOP codon in the spliceosome component Prpf8 (pre‐mRNA processing factor 8). Cph initially develops normally, but then develops widespread cell death, especially in neurons, and is embryonic lethal. Cph mutants accumulate aberrantly spliced transcripts retaining both U2‐ and U12‐type introns. Within early haematopoiesis, myeloid differentiation is impaired, suggesting Prpf8 is required for haematopoietic development. Cph provides an animal model for zygotic PRPF8 dysfunction diseases and for evaluating therapeutic interventions.
Does bromodomain flexibility influence histone recognition?
Authors: Steiner Sandra , Magno Andrea , Huang Danzhi , Caflisch Amedeo
Published: May 2013

Bromodomains are protein modules that selectively recognize histones by binding to acetylated lysines. Here, we have carried out multiple molecular dynamics simulations of 20 human bromodomains to investigate the flexibility of their binding site. Some bromodomains show alternative side chain orientations of three evolutionarily conserved residues: the Asn involved in acetyl‐lysine binding and two conserved aromatic residues. Furthermore, for the BAZ2B and CREBBP bromodomains we observe occlusion of the binding site which is coupled to the displacement of the two aromatic residues. In contrast to available structures, the simulations reveal large variability of the binding site accessibility. The simulations suggest that the flexibility of the bromodomain binding site and presence of self‐occluded metastable states influence the recognition of acetyl‐lysine on histone tails.
Cortical phase changes in Alzheimer's disease at 7T MRI: A novel imaging marker
Authors: van Rooden Sanneke , Versluis Maarten J. , Liem Michael K. , Milles Julien , Maier Andrea B. , Oleksik Ania M. , Webb Andrew G. , van Buchem Mark A. , van der Grond Jeroen
Published: May 2013

Background

Postmortem studies have indicated the potential of high‐field magnetic resonance imaging (MRI) to visualize amyloid depositions in the cerebral cortex. The aim of this study is to test this hypothesis in patients with Alzheimer's disease (AD).

Methods

T2*‐weighted MRI was performed in 16 AD patients and 15 control subjects. All magnetic resonance images were scored qualitatively by visual assessment, and quantitatively by measuring phase shifts in the cortical gray matter and hippocampus. Statistical analysis was performed to assess differences between groups.

Results

Patients with AD demonstrated an increased phase shift in the cortex in the temporoparietal, frontal, and parietal regions (P < .005), and this was associated with individual Mini‐Mental State Examination scores (r = −0.54, P < .05).

Conclusion

Increased cortical phase shift in AD patients demonstrated on 7‐tesla T2*‐weighted MRI is a potential new biomarker for AD, which may reflect amyloid pathology in the early stages.
Effect of APOE genotype status on targeted clinical trials outcomes and efficiency in dementia and mild cognitive impairment resulting from Alzheimer's disease
Authors: Kennedy Richard E. , Cutter Gary R. , Schneider Lon S.
Published: May 2013

Background

The apolipoprotein E (APOE) ε4 genotype has been recommended as a potential inclusion or exclusion criterion in targeted clinical trials for Alzheimer's disease (AD) and mild cognitive impairment (MCI) resulting from AD, and has been implemented in trials of immunotherapeutic agents.

Methods

We tested this recommendation with clinical trial simulations using participants from a meta‐database of 19 studies to create trial samples with APOE ε4 proportions ranging from 0% (all noncarriers) to 100% (all carriers). For each percentage of APOE ε4 carriers, we resampled the database randomly for 1000 trials for each trial scenario, planning for 18‐ or 24‐month trials with samples from 50 to 400 patients per treatment or placebo group, up to 40% dropouts, and outcomes on the Alzheimer's Disease Assessment Scale, cognitive subscale (ADAS‐cog) with effect sizes from 0.15 to 0.75, and calculated statistical power.

Results

Enrichment of clinical trial participants based on APOE ε4 carrier status resulted in minimal increases in power compared with enrolling participants with the APOE ε3 genotype only or enrolling patients without regard to APOE genotype. Increased screening requirements to enhance the sample would offset gains in power.

Conclusions

Although samples enriched for APOE ε4 carriers in AD or MCI clinical trials showed slightly more cognitive impairment and greater decline using the number APOE ε4 alleles as an inclusion criterion most likely would not result in more efficient trials, and trials would take longer because fewer patients would be available. The APOE ε4/εX (where X = 2, 3 or 4) genotype could be useful, however, as an explanatory variable or covariate if warranted by a drug's action.
Predictability of the simple technical trading rules: An out‐of‐sample test
Authors: Fang Jiali , Jacobsen Ben , Qin Yafeng
Published: May 2013

In a true out‐of‐sample test based on fresh data we find no evidence that several well‐known technical trading strategies predict stock markets over the period of 1987 to 2011. Our test safeguards against sample selection bias, data mining, hindsight bias, and other usual biases that may affect results in our field. We use the exact same technical trading rules thatBrock, Lakonishok, and LeBaron (1992)showed to work best in their historical sample. Further analysis shows that this poor out‐of‐sample performance most likely is not due to the market becoming more efficient – instantaneously or gradually over time – but probably a result of bias.
Epithelial neoplasia in
Drosophila
entails switch to primitive cell states
Authors: Khan Sumbul J. , Bajpai Anjali , Alam Mohammad Atif , Gupta Ram P. , Harsh Sneh , Pandey Ravi K. , Goel-Bhattacharya Surbhi , Nigam Aditi , Mishra Arati , Sinha Pradip
Published: May 2013

Significance

Not all cell types in a lineage hierarchy succumb to cancer in the face of an oncogenic lesion. What turns only select cells within an organ into “cells-of-origin” in cancer is an enduring riddle of cancer biology. Here we show that in epithelial primordia of adult wings and eyes of
Drosophila
, oncogenically mutated cells lose their developmental commitments and, instead, switch to a primitive or progenitor-like cell state. Switch-to-a-primitive-cell-state could thus be a prevalent mechanism of epithelial carcinogenesis and, possibly, an essential characteristic of cancer cells-of-origin.
Gate-tunable polarized phase of two-dimensional electrons at the LaAlO
3
/SrTiO
3
interface
Authors: Joshua Arjun , Ruhman Jonathan , Pecker Sharon , Altman Ehud , Ilani Shahal
Published: May 2013

Controlling the coupling between localized spins and itinerant electrons can lead to exotic magnetic states. A novel system featuring local magnetic moments and extended 2D electrons is the interface between LaAlO
3
and SrTiO
3
. The magnetism of the interface, however, was observed to be insensitive to the presence of these electrons and is believed to arise solely from extrinsic sources like oxygen vacancies and strain. Here we show the existence of unconventional electronic phases in the LaAlO
3
/SrTiO
3
system pointing to an underlying tunable coupling between itinerant electrons and localized moments. Using anisotropic magnetoresistance and anomalous Hall effect measurements in a unique in-plane configuration, we identify two distinct phases in the space of carrier density and magnetic field. At high densities and fields, the electronic system is strongly polarized and shows a response, which is highly anisotropic along the crystalline directions. Surprisingly, below a density-dependent critical field, the polarization and anisotropy vanish whereas the resistivity sharply rises. The unprecedented vanishing of the easy axes below a critical field is in sharp contrast with other coupled magnetic systems and indicates strong coupling with the moments that depends on the symmetry of the itinerant electrons. The observed interplay between the two phases indicates the nature of magnetism at the LaAlO
3
/SrTiO
3
interface as both having an intrinsic origin and being tunable.
Nontransformed, GM-CSF–dependent macrophage lines are a unique model to study tissue macrophage functions
Authors: Fejer György , Wegner Mareike Dorothee , Györy Ildiko , Cohen Idan , Engelhard Peggy , Voronov Elena , Manke Thomas , Ruzsics Zsolt , Dölken Lars , Prazeres da Costa Olivia , Branzk Nora , Huber Michael , Prasse Antje , Schneider Robert , Apte Ron N. , Galanos Chris , Freudenberg Marina A.
Published: May 2013

Significance

Macrophages—cells crucially involved in defense against infections—exhibit, depending on their anatomical location, distinct biological properties. Studies of the underlying mechanisms are of scientific and clinical interest, but are hampered by the difficulty of obtaining primary tissue macrophages in sufficient numbers and purity. Here, we report the generation of nontransformed murine macrophages, which are similar to alveolar macrophages and can be grown continuously without change of phenotype and in unlimited amounts. Such macrophages helped us to recognize several innate immune properties of alveolar macrophages that are involved in the pathogenesis of infectious lung inflammation.
Are Results from Non‐hypothetical Choice‐based Conjoint Analyses and Non‐hypothetical Recoded‐ranking Conjoint Analyses Similar?
Authors: Akaichi Faical , Nayga Rodolfo M. , Gil José M.
Published: May 2013

Conflicting findings have been found in previous research that compared choice‐based conjoint analysis and ranking conjoint analysis in a public good setting. The present paper revisits this issue for a private good in a non‐hypothetical context using small and large choice sets. Our results suggest that in a small choice set setting, participants' preferences and willingness to pay are similar across the two conjoint analysis formats. However, in large choice sets, a divergence between the two conjoint analysis formats emerges. Hence, the two conjoint analysis formats can only be used interchangeably in small choice sets, not in large choice sets.
viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
Authors: Watson Mick , Schnettler Esther , Kohl Alain
Published: May 2013

Summary: RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports.

Availability and implementation: viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome.

Contact:  mick.watson@roslin.ed.ac.uk
PIUS: peptide identification by unbiased search
Authors: Costa Eduardo P. , Menschaert Gerben , Luyten Walter , De Grave Kurt , Ramon Jan
Published: May 2013

Summary: We present PIUS, a tool that identifies peptides from tandem mass spectrometry data by analyzing the six-frame translation of a complete genome. It differs from earlier studies that have performed such a genomic search in two ways: (i) it considers a larger search space and (ii) it is designed for natural peptide identification rather than proteomics. Differently from other peptidomics tools designed for genome-wide searches, PIUS does not limit the analysis to a set of sequences that match a list of de novo reconstructions.

Availability: Source code, executables and a detailed technical report are freely available at http://dtai.cs.kuleuven.be/ml/systems/pius.

Contact:  eduardo.costa@cs.kuleuven.be

Supplementary information: Supplementary data are available at Bioinformatics online.
Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
Authors: Hon Jiří , Martínek Tomáš , Rajdl Kamil , Lexa Matej
Published: May 2013

Motivation: Upgrade and integration of triplex software into the R/Bioconductor framework.

Results: We combined a previously published implementation of a triplex DNA search algorithm with visualization to create a versatile R/Bioconductor package ‘triplex’. The new package provides functions that can be used to search Bioconductor genomes and other DNA sequence data for occurrence of nucleotide patterns capable of forming intramolecular triplexes (H-DNA). Functions producing 2D and 3D diagrams of the identified triplexes allow instant visualization of the search results. Leveraging the power of Biostrings and GRanges classes, the results get fully integrated into the existing Bioconductor framework, allowing their passage to other Genome visualization and annotation packages, such as GenomeGraphs, rtracklayer or Gviz.

Availability: R package ‘triplex’ is available from Bioconductor (bioconductor.org).

Contact:  lexa@fi.muni.cz

Supplementary information:  Supplementary data are available at Bioinformatics online.
Polaribacter sejongensis sp. nov., isolated from Antarctic soil, and emended descriptions of the genus

Polaribacter

,

Polaribacter butkevichii

and

Polaribacter irgensii
Authors: Kim Byung-Chun , Oh Hyun Woo , Kim Hyangmi , Park Doo-Sang , Hong Soon Gyu , Lee Hong Kum , Bae Kyung Sook
Published: May 2013

A Gram-staining-negative, catalase- and oxidase-positive, non-motile bacterium, designated strain KOPRI 21160T, was isolated from Antarctic soil. Based on 16S rRNA gene sequence analysis, strain KOPRI 21160T was found to belong to the genus

Polaribacter

. Sequence similarity between strain KOPRI 21160T and the type strains of species of the genus

Polaribacter

was 94.2–98.3 %. The nearest phylogenetic neighbours of strain KOPRI 21160T were

Polaribacter butkevichii

KCTC 12100T (98.3 % similarity) and

Polaribacter irgensii

KCTC 23136T (97.5 %). DNA–DNA relatedness was 50.6 %, between strain KOPRI 21160T and

P. butkevichii

KCTC 12100T, and 45.2 % between strain KOPRI 21160T and

P. irgensii

KCTC 23136T. Strain KOPRI 21160T grew at 4–37 °C and at pH 7.0–8.5. It could hydrolyse DNA, starch and Tweens 20, 40, 60 and 80. Menaquinone-6 (MK-6) was the only respiratory quinone, and iso-C15 : 0, iso-C15 : 0 3-OH and C15 : 1ω6c were the major cellular fatty acids. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The DNA G+C content was 30.0 mol%. Based on data from our polyphasic study, the organism is considered to represent a novel species of the genus

Polaribacter

, for which we propose the name Polaribacter sejongensis sp. nov. The type strain is KOPRI 21160T ( = KCTC 23670T = JCM 18092T). Emended descriptions of the genus

Polaribacter

,

Polaribacter butkevichii

Nedashkovskaya et al. 2005 and

Polaribacter irgensii

Gosink et al. 1998 are also proposed.
Aquamicrobium aestuarii sp. nov., a marine bacterium isolated from a tidal flat
Authors: Jin Hyun Mi , Kim Jeong Myeong , Jeon Che Ok
Published: May 2013

A Gram-negative, strictly aerobic, motile bacterium with flagella, designated strain G210T, was isolated from a crude-oil-contaminated tidal flat of the Taean coast in South Korea. Cells were non-spore-forming, ovoid rods showing catalase- and oxidase-positive reactions. Growth of strain G210T was observed between 15 and 45 °C (optimum, 30–35 °C) and between pH 5.5 and 9.0 (optimum, pH 6.5–7.5). Strain G210T contained Q-10 as the sole isoprenoid quinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c as the major fatty acids. Putrescine and spermidine were identified as the major polyamines. Strain G210T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, an unidentified phospholipid and an unidentified aminolipid as polar lipids. The G+C content of the genomic DNA was 56.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G210T formed a phyletic lineage with members of the genus

Aquamicrobium

. Strain G210T was most closely related to

Aquamicrobium ahrensii

905/1T (97.9 % similarity). The DNA–DNA relatedness between strain G210T and the type strain of

A. ahrensii

was 24±0.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G210T represents a novel species within the genus

Aquamicrobium

, for which the name Aquamicrobium aestuarii sp. nov. is proposed. The type strain is G210T ( = KACC 14931T = JCM 16876T).
Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules
Authors: De Meyer Sofie E. , Cnockaert Margo , Ardley Julie K. , Maker Garth , Yates Ron , Howieson John G. , Vandamme Peter
Published: May 2013

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus

Burkholderia

, with the representative strain WSM5005T being most closely related to

Burkholderia tuberum

(98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus

Burkholderia

. Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus

Burkholderia

with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.
Citeromyces nyonsensis sp. nov., a novel yeast species isolated from black olive brine
Authors: Casaregola Serge , Jacques Noémie , Louis-Mondesir Christelle , Coton Monika , Coton Emmanuel
Published: May 2013

A yeast strain was isolated from olive brines in a fermented black olive and olive oil manufacturing plant in the town of Nyons (France). On the basis of domains 1 and 2 (D1/D2) large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region sequence analyses, the strain CLIB 1303T was found to be closely related, but clearly distinct, from the three existing species of the genus Citeromyces: Citeromyces matritensis, Citeromyces siamensis and Citeromyces haiwaiiensis. Strain CLIB 1303T exhibited 6 bp, 7 bp and 12 bp divergences in the D1/D2 LSU rRNA gene with C. siamensis, C. matritensis and C. hawaiiensis, respectively. ITS region divergence amounted to more than 8 %, 4 % and 4.5 % with C. siamensis, C. matritensis and C. hawaiiensis, respectively, in addition to several indels. Like C. matritensis and C. siamensis strains, strain CLIB 1303T was shown to be halotolerant and osmotolerant. Phenotypically, strain CLIB 1303T can be distinguished from other species of the genus Citeromyces by its inability to assimilate trehalose. The strain CLIB 1303T ( = CBS 12700T) was assigned to a novel species, Citeromyces nyonsensis sp. nov.
Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium
Authors: Hedrich Sabrina , Johnson D. Barrie
Published: May 2013

Twelve strains of iron-oxidizing acidithiobacilli isolated from acidic sites throughout the world, including some previously shown by multi-locus sequence analyses and DNA–DNA hybridization to comprise a distinct species, were characterized in terms of their physiologies. The bacteria were shown to be obligately chemolithotrophic, acidophilic and mesophilic, and grew in both oxic and anoxic environments, using ferrous iron, reduced sulfur or hydrogen as electron donors and oxygen or ferric iron as electron acceptors. Some of the strains grew at lower pH than those reported for the two recognized iron-oxidizingAcidithiobacillusspecies,Acidithiobacillus ferrooxidansandAcidithiobacillus ferrivorans. Tolerance of transition metals and aluminium, and also specific rates of iron oxidation and reduction, were more similar to those ofA. ferrooxidans(to which the strains are more closely related) than toA. ferrivorans. The nameAcidithiobacillus ferriduranssp. nov. is proposed to accommodate the 12 strains, with the type strain being JCM 18981T( = ATCC 33020T).
Verrucosispora andamanensis sp. nov., isolated from a marine sponge
Authors: Supong Khomsan , Suriyachadkun Chanwit , Suwanborirux Khanit , Pittayakhajonwut Pattama , Thawai Chitti
Published: May 2013

An actinomycete strain, SP03-05T, was isolated from a marine sponge sample (Xestospongia sp.) collected from Phuket Province of Thailand. The strain was aerobic, Gram-stain-positive and produced single spores at the tips of the substrate mycelium. Strain SP03-05T contained meso-diaminopimelic acid in the peptidoglycan; whole-cell sugars were arabinose, galactose, glucose, rhamnose, ribose and xylose. The polar lipid profile of strain SP03-05T consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and unknown polar lipids. Morphological and chemotaxonomic characteristics of the strain identified it as a member of the family

Micromonosporaceae

. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity of the strain to

Verrucosispora lutea

YIM 013T (96.90 %),

Verrucosispora sediminis

MS426T (96.90 %),

Verrucosispora gifhornensis

DSM 44337T (96.80 %),

Verrucosispora maris

AB-18-032T (96.80 %) and

Verrucosispora qiuiae

RtIII47T (95.40 %). The DNA G+C content was 72.4 mol%. The phenotypic, genotypic and DNA–DNA hybridization results supported the classification of this strain as a representative of a novel species in the genus

Verrucosispora

, for which the name Verrucosispora andamanensis sp. nov. is proposed. The type strain is SP03-05T ( = BCC 45620T = NBRC 109075T).
Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences
Authors: Urbanczyk Henryk , Ogura Yoshitoshi , Hayashi Tetsuya
Published: May 2013

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.
Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter
Authors: Zhao Jian-Kang , Li Xiao-Ming , Zhang Ming-Jiang , Jin Jing-hua , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: May 2013

A novel pyrene-degrading, Gram-negative bacterium, designated strain P-4T, was isolated from a polycyclic aromatic hydrocarbon-degrading enrichment of polluted soils from a coking chemical plant. Cells of strain P-4Twere non-motile rods. Strain P-4Tgrew at 15–45 °C (optimum, 37 °C), pH 6.0–10.0 (optimum, pH 8.5) and 0–4 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence showed that strain P-4Twas related phylogenetically to members of the genusParapedobacter, with sequence similarity of 93.7–95.1 %. The cellular fatty acids of strain P-4Twere iso-C15 : 0, summed feature 3 (C16 : 1ω7cand/or C16 : 1ω6c), iso-C17 : 03-OH, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), anteiso-C15 : 0, iso-C15 : 03-OH, C16 : 0, iso-C15 : 1G, C16 : 03-OH and C17 : 02-OH. Cells contained menaquinone 7 as the major quinone. The polyamine of strain P-4Twas homospermidine, and the main polar lipids were phosphatidylethanolamine and a sphingolipid. The G+C content of the DNA was 45.4 mol%. Strain P-4Tshowed a range of phenotypic characteristics that differentiated it from previously recognizedParapedobacterspecies, particularly its ability to use pyrene as a sole carbon source for growth and its alkaline optimal pH for growth (pH 8.5). On the basis of these results, it is concluded that strain P-4Trepresents a novel species of the genusParapedobacter, for which the nameParapedobacter pyrenivorans(type strain P-4T = NBRC 109113T = CGMCC 1.12195T) is proposed. An emended description of the genusParapedobacteris also provided.
Wickerhamiella slavikovae sp. nov. and Wickerhamiella goesii sp. nov., two yeast species isolated from natural substrates
Authors: Hagler Allen N. , Ribeiro José R. A. , Pinotti T. , Brandão Luciana R. , Pimenta Raphael S. , Lins U. , Lee Ching-Fu , Hsieh Chin-Wen , Lachance Marc-André , Rosa Carlos A.
Published: May 2013

Two novel yeast species were isolated during three independent studies of yeasts associated with natural substrates in Brazil and Taiwan. Analysis of the sequences of the D1/D2 domains of the large subunit rRNA gene showed that these novel species belong to the Wickerhamiella clade. The first was isolated from freshwater and a leaf of sugar cane (Saccharum officinarum) in Brazil and from leaves of Wedelia biflora in Taiwan. Described here as Wickerhamiella slavikovae sp. nov., it differs by 56 nucleotide substitutions and 19 gaps in the D1/D2 region of the large subunit rRNA gene from Candida sorbophila, the least divergent species. The second species, named Wickerhamiella goesii sp. nov., was isolated from leaves and the rhizosphere of sugar cane collected in Rio de Janeiro, Brazil. The species differs by 54 nucleotide substitutions and nine gaps in the D1/D2 domains from Candida drosophilae, its least divergent relative. The type strains are Wickerhamiella slavikovae sp. nov. IMUFRJ 52096T ( = CBS 12417T = DBVPG 8032T) and Wickerhamiella goesii sp. nov. IMUFRJ 52102T ( = CBS 12419T = DBVPG 8034T).
The yeast genus Tortispora gen. nov., description of Tortispora ganteri sp. nov., Tortispora mauiana f.a., sp. nov., Tortispora agaves f.a., sp. nov., Tortispora sangerardonensis f.a., sp. nov., Tortispora cuajiniquilana f.a., sp. nov., Tortispora starmeri f.a., sp. nov. and Tortispora phaffii f.a., sp. nov., reassignment of Candida caseinolytica to Tortispora caseinolytica f.a., comb. nov., emendation of Botryozyma, and assignment of Botryozyma, Tortispora gen. nov. and Trigonopsis to the family Trigonopsidaceae fam. nov.
Authors: Lachance M.-A. , Kurtzman C. P.
Published: May 2013

We describe the yeast genus Tortispora gen. nov., an early-diverging lineage in the Saccharomycetales that displays the formation of helical ascospores. The genus is based on 16 strains resembling Candida caseinolytica that were isolated from necrotic plant tissue in warm regions of the New World. Based on sequences of the D1/D2 domains of the nuclear large subunit rRNA gene, as well as other data, the strains are assigned to eight distinct species. The species are nutritionally specialized and share the unusual ability to hydrolyse casein and to grow on 1-butanol as sole carbon source. One species of the proposed new genus produces a simple ascus with a helical ascospore, whereas other species of the clade have failed to form ascospores. All species in the clade, including C. caseinolytica, are assigned to Tortispora gen. nov. The new binomials are Tortispora ganteri sp. nov., type species of the genus (SUB 86-469.5T  = CBS 12581T  = NRRL Y-17035T), Tortispora caseinolytica f.a., comb. nov. (UCD-FST 83-438.3T  = CBS 7781T  = NRRL Y-17796T), Tortispora mauiana f.a., sp. nov. (UWOPS 87-2430.3T  = CBS 12803T  = NRRL Y-48832T), Tortispora agaves f.a., sp. nov. (UWOPS 94-257.6T  = CBS 12794T  = NRRL Y-63662T), Tortispora sangerardonensis f.a., sp. nov. (UWOPS 00-157.1T  = CBS 12795T  = NRRL Y-63663T), Tortispora cuajiniquilana f.a., sp. nov. (UWOPS 99-344.4T  = CBS 12796T  = NRRL Y-63664T), Tortispora starmeri f.a., sp. nov. (G 91-702.5T  = CBS 12793T  = NRRL Y-63665T) and Tortispora phaffii f.a., sp. nov. (UWOPS 91-445.1T  = CBS 12804T  = NRRL Y-48833T). In addition, species formerly assigned to the genus Ascobotryozyma are reassigned to the genus Botryozyma. The genera Trigonopsis, Botryozyma and Tortispora are assigned to the family Trigonopsidaceae fam. nov.
Gracilimonas rosea sp. nov., isolated from tropical seawater, and emended description of the genus

Gracilimonas
Authors: Cho Yirang , Chung Hyunwoo , Jang Gwang Il , Choi Dong Han , Noh Jae Hoon , Cho Byung Cheol
Published: May 2013

A Gram-staining-negative, non-motile, spore-forming, rod-shaped, marine bacterial strain, CL-KR2T, was isolated from tropical seawater near Kosrae, an island in the Federated States of Micronesia. Analysis of the 16S rRNA gene sequence of strain CL-KR2T revealed a clear affiliation with the genus

Gracilimonas

. Based on phylogenetic analysis, strain CL-KR2T showed the closest phylogenetic relationship to

Gracilimonas tropica

CL-CB462T, with 16S rRNA gene sequence similarity of 96.6 %. DNA–DNA relatedness between strain CL-KR2T and

G. tropica

CL-CB462T was 6.7 % (reciprocal 9.5 %). Strain CL-KR2T grew in the presence of 1–20 % sea salts and the optimal salt concentration was 3.5–5 %. The temperature and pH optima for growth were 35 °C and pH 7.5. The major cellular fatty acids (≥10.0 %) of strain CL-KR2T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 1ω9c and the only isoprenoid quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, two unidentified glycolipids and two unidentified lipids. The genomic DNA G+C content of strain CL-KR2T was 43.2 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain CL-KR2T could be distinguished from the only member of the genus

Gracilimonas

with a validly published name. Thus, strain CL-KR2T should be assigned to a novel species in the genus

Gracilimonas

, for which the name Gracilimonas rosea sp. nov. is proposed. The type strain is CL-KR2T ( = KCCM 90206T = JCM 18898T).
Rothia

endophytica sp. nov., an actinobacterium isolated from Dysophylla stellata (Lour.) Benth
Authors: Xiong Zi-Jun , Zhang Jin-Li , Zhang Dao-Feng , Zhou Zhi-Li , Liu Min-Jiao , Zhu Wen-Yong , Zhao Li-Xing , Xu Li-Hua , Li Wen-Jun
Published: May 2013

A novel endophytic actinobacterium, designated strain YIM 67072T, was isolated from healthy roots of Dysophylla stellata (Lour.) Benth. Cells of this aerobic, cream–yellow-coloured strain occurred singly, in pairs or in tetrads, were Gram-stain-positive and ovoid- to spherical-shaped. Strain YIM 67072T grew at 4–45 °C, pH 5.0–10.0 and in the presence of 0–7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 67072T belonged to the genus

Rothia

. The isolate contained MK-7 as the major component of the quinone system. The peptidoglycan type was A3α. The polar lipid profile consisted predominantly of diphosphatidylglycerol and glycolipids. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 53.2 mol%. However, strain YIM 67072T differed from its closest relatives

Rothia nasimurium

CCUG 35957T (98.5 % 16S rRNA gene sequence similarity),

Rothia amarae

JCM 11375T (97.6 %) and

Rothia terrae

L-143T (97.3 %) in many phenotypic characteristics. Moreover, the levels of DNA–DNA relatedness between the novel isolate and the three above-mentioned type strains were 28.7±1.3 %, 36.5±1.2 %, 46.8±1.5 %, respectively. Based on comparative analysis of physiological and chemotaxonomic data, strain YIM 67072T represents a novel species of the genus

Rothia

, for which the name

Rothia

endophytica sp. nov. is proposed. The type strain is YIM 67072T ( = DSM 26247T = JCM 18541T).
The reassignment of three ‘lost’ Taphrina species (Taphrina bullata, Taphrina insititiae and Taphrina rhizophora) supported by the divergence of nuclear and mitochondrial DNA
Authors: Petrýdesová Jana , Bacigálová Kamila , Sulo Pavol
Published: May 2013

The ascomycetous genus Taphrina Fries originally contained more than 90 phytopathogenic microscopic dimorphic ascomycetes causing specific infections in different vascular plants. Although species have mainly been identified historically according to their host and morphological and physiological traits, they can be studied and preserved in the form of yeasts arising from germinating ascospores. Due to low DNA sequence divergence and the lack of available strains, the number of accepted Taphrina species has currently been reduced to 28. The aim of this study is the description of three previously accepted species. Taphrina bullata (type strain CCY 58-4-1 = CBS 12783), Taphrina insititiae (type strain CCY 58-5-1 = CBS 12782) and Taphrina rhizophora (type strain CCY 58-6-1 = CBS 12781), which have been omitted from a recent key. The host range, the divergence of the 26S rRNA gene sequence, internal transcribed spacers (ITS) and the mitochondrial small ribosomal subunit (rns) sequence strongly support their reassignment as species.
Abscisic Acid Mediates a Divergence in the Drought Response of Two Conifers
Authors: Brodribb Timothy J. , McAdam Scott A.M.
Published: May 2013

During water stress, stomatal closure occurs as water tension and levels of abscisic acid (ABA) increase in the leaf, but the interaction between these two drivers of stomatal aperture is poorly understood. We investigate the dynamics of water potential, ABA, and stomatal conductance during the imposition of water stress on two drought-tolerant conifer species with contrasting stomatal behavior. Rapid rehydration of excised shoots was used as a means of differentiating the direct influences of ABA and water potential on stomatal closure. Pinus radiata (Pinaceae) was found to exhibit ABA-driven stomatal closure during water stress, resulting in strongly isohydric regulation of water loss. By contrast, stomatal closure in Callitris rhomboidea (Cupressaceae) was initiated by elevated foliar ABA, but sustained water stress saw a marked decline in ABA levels and a shift to water potential-driven stomatal closure. The transition from ABA to water potential as the primary driver of stomatal aperture allowed C. rhomboidea to rapidly recover gas exchange after water-stressed plants were rewatered, and was associated with a strongly anisohydric regulation of water loss. These two contrasting mechanisms of stomatal regulation function in combination with xylem vulnerability to produce highly divergent strategies of water management. Species-specific ABA dynamics are proposed as a central component of drought survival and ecology.
A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins
Authors: Campos Bruna Medéia , Sforça Mauricio Luis , Ambrosio Andre Luis Berteli , Domingues Mariane Noronha , Brasil de Souza Tatiana de Arruda Campos , Barbosa João Alexandre Ribeiro Gonçalvez , Leme Adriana Franco Paes , Perez Carlos Alberto , Whittaker Sara Britt-Marie , Murakami Mario Tyago , Zeri Ana Carolina de Matos , Benedetti Celso Eduardo
Published: May 2013

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.
D6PK AGCVIII Kinases Are Required for Auxin Transport and Phototropic Hypocotyl Bending in Arabidopsis
Authors: Willige Björn C. , Ahlers Siv , Zourelidou Melina , Barbosa Inês C.R. , Demarsy Emilie , Trevisan Martine , Davis Philip A. , Roelfsema M. Rob G. , Hangarter Roger , Fankhauser Christian , Schwechheimer Claus
Published: May 2013

Phototropic hypocotyl bending in response to blue light excitation is an important adaptive process that helps plants to optimize their exposure to light. In Arabidopsis thaliana, phototropic hypocotyl bending is initiated by the blue light receptors and protein kinases phototropin1 (phot1) and phot2. Phototropic responses also require auxin transport and were shown to be partially compromised in mutants of the PIN-FORMED (PIN) auxin efflux facilitators. We previously described the D6 PROTEIN KINASE (D6PK) subfamily of AGCVIII kinases, which we proposed to directly regulate PIN-mediated auxin transport. Here, we show that phototropic hypocotyl bending is strongly dependent on the activity of D6PKs and the PIN proteins PIN3, PIN4, and PIN7. While early blue light and phot-dependent signaling events are not affected by the loss of D6PKs, we detect a gradual loss of PIN3 phosphorylation in d6pk mutants of increasing complexity that is most severe in the d6pk d6pkl1 d6pkl2 d6pkl3 quadruple mutant. This is accompanied by a reduction of basipetal auxin transport in the hypocotyls of d6pk as well as in pin mutants. Based on our data, we propose that D6PK-dependent PIN regulation promotes auxin transport and that auxin transport in the hypocotyl is a prerequisite for phot1-dependent hypocotyl bending.