bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-Scale Analyses of Glycosylation in Cellulases
Authors: Zhou Fengfeng , Olman Victor , Xu Ying
Published: February 2010

Cellulases are important glycosyl hydrolases (GHs) that hydrolyze cellulose polymers into smaller oligosaccharides by breaking the cellulose β (1→4) bonds, and they are widely used to produce cellulosic ethanol from the plant biomass. N-linked and O-linked glycosylations were proposed to impact the catalytic efficiency, cellulose binding affinity and the stability of cellulases based on observations of individual cellulases. As far as we know, there has not been any systematic analysis of the distributions of N-linked and O-linked glycosylated residues in cellulases, mainly due to the limited annotations of the relevant functional domains and the glycosylated residues. We have computationally annotated the functional domains and glycosylated residues in cellulases, and conducted a systematic analysis of the distributions of the N-linked and O-linked glycosylated residues in these enzymes. Many N-linked glycosylated residues were known to be in the GH domains of cellulases, but they are there probably just by chance, since the GH domain usually occupies more than half of the sequence length of a cellulase. Our analysis indicates that the O-linked glycosylated residues are significantly enriched in the linker regions between the carbohydrate binding module (CBM) domains and GH domains of cellulases. Possible mechanisms are discussed.
A Modified Ant Colony Optimization Algorithm for Tumor Marker Gene Selection
Authors: Yu Hualong , Gu Guochang , Liu Haibo , Shen Jing , Zhao Jing
Published: February 2010

Microarray data are often extremely asymmetric in dimensionality, such as thousands or even tens of thousands of genes but only a few hundreds of samples or less. Such extreme asymmetry between the dimensionality of genes and samples can lead to inaccurate diagnosis of disease in clinic. Therefore, it has been shown that selecting a small set of marker genes can lead to improved classification accuracy. In this paper, a simple modified ant colony optimization (ACO) algorithm is proposed to select tumor-related marker genes, and support vector machine (SVM) is used as classifier to evaluate the performance of the extracted gene subset. Experimental results on several benchmark tumor microarray datasets showed that the proposed approach produces better recognition with fewer marker genes than many other methods. It has been demonstrated that the modified ACO is a useful tool for selecting marker genes and mining high dimension data.
Bioorganometallic mechanism of action, and inhibition, of IspH
Authors: Wang Weixue , Wang Ke , Liu Yi-Liang , No Joo-Hwan , Li Jikun , Nilges Mark J. , Oldfield Eric
Published: February 2010

We have investigated the mechanism of action of
Aquifex aeolicus
IspH [E-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) reductase], together with its inhibition, using a combination of site-directed mutagenesis (
K

M

,
V
max
), EPR and
1
H,
2
H,
13
C,
31
P, and
57
Fe-electron-nuclear double resonance (ENDOR) spectroscopy. On addition of HMBPP to an (unreactive) E126A IspH mutant, a reaction intermediate forms that has a very similar EPR spectrum to those seen previously with the HMBPP “parent” molecules, ethylene and allyl alcohol, bound to a nitrogenase FeMo cofactor. The EPR spectrum is broadened on
57
Fe labeling and there is no evidence for the formation of allyl radicals. When combined with ENDOR spectroscopy, the results indicate formation of an organometallic species with HMBPP, a
π
/
σ
“metallacycle” or
η
2
-alkenyl complex. The complex is poised to interact with H
+
from E126 (and H124) in reduced wt IspH, resulting in loss of water and formation of an
η
1
-allyl complex. After reduction, this forms an
η
3
-allyl
π
-complex (i.e. containing an allyl anion) that on protonation (at C2 or C4) results in product formation. We find that alkyne diphosphates (such as propargyl diphosphate) are potent IspH inhibitors and likewise form metallacycle complexes, as evidenced by
1
H,
2
H, and
13
C ENDOR, where hyperfine couplings of approximately 6 MHz for
13
C and 10 MHz for
1
H, are observed. Overall, the results are of broad general interest because they provide new insights into IspH catalysis and inhibition, involving organometallic species, and may be applicable to other Fe
4
S
4
-containing proteins, such as IspG.
Molecular mechanism of the sweet taste enhancers
Authors: Zhang Feng , Klebansky Boris , Fine Richard M. , Liu Haitian , Xu Hong , Servant Guy , Zoller Mark , Tachdjian Catherine , Li Xiaodong
Published: February 2010

Positive allosteric modulators of the human sweet taste receptor have been developed as a new way of reducing dietary sugar intake. Besides their potential health benefit, the sweet taste enhancers are also valuable tool molecules to study the general mechanism of positive allosteric modulations of T1R taste receptors. Using chimeric receptors, mutagenesis, and molecular modeling, we reveal how these sweet enhancers work at the molecular level. Our data argue that the sweet enhancers follow a similar mechanism as the natural umami taste enhancer molecules. Whereas the sweeteners bind to the hinge region and induce the closure of the Venus flytrap domain of T1R2, the enhancers bind close to the opening and further stabilize the closed and active conformation of the receptor.
RFWD3–Mdm2 ubiquitin ligase complex positively regulates p53 stability in response to DNA damage
Authors: Fu Xiaoyong , Yucer Nur , Liu Shangfeng , Li Muyang , Yi Ping , Mu Jung-Jung , Yang Tao , Chu Jessica , Jung Sung Yun , O’Malley Bert W. , Gu Wei , Qin Jun , Wang Yi
Published: February 2010

In unstressed cells, the tumor suppressor p53 is maintained at low levels by ubiquitin-mediated proteolysis mainly through Mdm2. In response to DNA damage, p53 is stabilized and becomes activated to turn on transcriptional programs that are essential for cell cycle arrest and apoptosis. Activation of p53 leads to accumulation of Mdm2 protein, a direct transcriptional target of p53. It is not understood how p53 is protected from degradation when Mdm2 is up-regulated. Here we report that p53 stabilization in the late phase after ionizing radiation correlates with active ubiquitination. We found that an E3 ubiquitin ligase RFWD3 (RNF201/FLJ10520) forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and is required to stabilize p53 in the late response to DNA damage. This process is regulated by the DNA damage checkpoint, because RFWD3 is phosphorylated by ATM/ATR kinases and the phosphorylation mutant fails to stimulate p53 ubiquitination. In vitro experiments suggest that RFWD3 is a p53 E3 ubiquitin ligase and that RFWD3–Mdm2 complex restricts the polyubiquitination of p53 by Mdm2. Our study identifies RFWD3 as a positive regulator of p53 stability when the G
1
cell cycle checkpoint is activated and provides an explanation for how p53 is protected from degradation in the presence of high levels of Mdm2.
Röntgen’s electrode-free elastomer actuators without electromechanical pull-in instability
Authors: Keplinger Christoph , Kaltenbrunner Martin , Arnold Nikita , Bauer Siegfried
Published: February 2010

Electrical actuators made from films of dielectric elastomers coated on both sides with stretchable electrodes may potentially be applied in microrobotics, tactile and haptic interfaces, as well as in adaptive optical elements. Such actuators with compliant electrodes are sensitive to the pull-in electromechanical instability, limiting operational voltages and attainable deformations. Electrode-free actuators driven by sprayed-on electrical charges were first studied by Röntgen in 1880. They withstand much higher voltages and deformations and allow for electrically clamped (charge-controlled) thermodynamic states preventing electromechanical instabilities. The absence of electrodes allows for direct optical monitoring of the actuated elastomer, as well as for designing new 3D actuator configurations and adaptive optical elements.
Sampling the N-terminal proteome of human blood
Authors: Wildes David , Wells James A.
Published: February 2010

The proteomes of blood plasma and serum represent a potential gold mine of biological and diagnostic information, but challenges such as dynamic range of protein concentration have hampered efforts to unlock this resource. Here we present a method to label and isolate N-terminal peptides from human plasma and serum. This process dramatically reduces the complexity of the sample by eliminating internal peptides. We identify 772 unique N-terminal peptides in 222 proteins, ranging over six orders of magnitude in abundance. This approach is highly suited for studying natural proteolysis in plasma and serum. We find internal cleavages in plasma proteins created by endo- and exopeptidases, providing information about the activities of proteolytic enzymes in blood, which may be correlated with disease states. We also find signatures of signal peptide cleavage, coagulation and complement activation, and other known proteolytic processes, in addition to a large number of cleavages that have not been reported previously, including over 200 cleavages of blood proteins by aminopeptidases. Finally, we can identify substrates from specific proteases by exogenous addition of the protease combined with N-terminal isolation and quantitative mass spectrometry. In this way we identified proteins cleaved in human plasma by membrane-type serine protease 1, an enzyme linked to cancer progression. These studies demonstrate the utility of direct N-terminal labeling by subtiligase to identify and characterize endogenous and exogenous proteolysis in human plasma and serum.
Thermal stability of ionic liquid in confined geometry
Authors: Singh Manish Pratap , Singh Rajendra Kumar , Chandra Suresh
Published: February 2010

The thermal stability of imidazolium based ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMI][PF6]) in a confined geometry is analysed. It has been found that the decomposition of IL starts at an earlier temperature upon confinement in nanopores. Early decomposition of confined IL is due to the breaking of end group alkyl chains of the [BMI] ring, which is explained by a phenomenological ‘hinged spring’ model.
Characteristics of internal inductively coupled plasma with a ferrite module
Authors: Lim Jong Hyeuk , Kim Kyong Nam , Gwon Gwang Ho , Hong Seng Pyo , Kim Seok Hwan , Yeom Geun Young
Published: February 2010

The electrical and plasma properties of an internal inductively coupled plasma system with and without a Ni–Zn ferrite module operated at 13.56 and 2 MHz were investigated. Installing a ferrite module covering the top half of the ICP antenna increased the inductive coupling of the antenna to the plasma by the magnetic field reinforced by the ferrite. However, because of the high impedance of the Ni–Zn ferrite operated at 13.56 MHz, a more effective coupling was achieved at the operational frequency of 2 MHz. By using the ferrite module at 2 MHz, a plasma density of ∼6 × 1011 cm−3 and a plasma potential of ∼13 V were obtained at 500 W and 5 mTorr Ar. The plasma density was higher and the plasma potential lower than those obtained at 13.56 MHz.
Hybrid particle-in-cell (PIC) ions and Boltzmann electron distribution simulation of direct-current plasma immersion ion implantation into three-dimensional objects
Authors: Kwok Dixon T K , Li Jianhui , Ma Xiaobo , Chu Paul K
Published: February 2010

A hybrid protocol including particle-in-cell (PIC) ions and Boltzmann electron distribution is developed to simulate plasma immersion ion implantation (PIII) into an S-shaped bar inside a grounded cylindrical cage consisting of a mesh. A multiple-grid system with three cell confinements is adopted to achieve sufficient accuracy and acceptable computational time. The simulation results reveal that the implantation fluence distribution along the major curvature is more uniform than that obtained by conventional PIII.
Hydrophilic and optical properties of nanostructured titania prepared by sol–gel dip coating
Authors: Ferrara M C , Pilloni L , Mazzarelli S , Tapfer L
Published: February 2010

Nanostructured titania thin films were prepared under controlled atmospheric conditions by the sol–gel dip-coating technique on glass, fused silica and (1 0 0)-silicon substrates. Two different sol–gel routes were employed by using different precursor solutions, a highly acid solution and a polymer-like solution. The influence of sol composition and of the substrate type on the morphology, coating porosity, surface roughness, crystalline phases and grain size of the titania films were investigated in detail. In addition, the relationship between microstructural/morphological properties and the optical properties (energy gap, refractive index and extinction coefficient) and the hydrophilic performance of the coatings were evaluated. Our experimental results clearly indicate that the sol composition and substrate type remarkably influence the films' morphology and microstructure; moreover, they consequently modify the optical response and hydrophilic performances of the samples, showing that superhydrophilic titania coatings can be obtained opportunely by choosing the composition of the precursor sol–gel solution. Blue shift of the band gap energy and a band structure mutation from indirect to direct were also revealed. The hydrophilic properties and the change in the band gaps transition can be attributed to oxygen vacancies on the surface of the titania nanocrystallites that gives rise to Ti3+ sites and, consequently, to structural changes/defects of the anatase nanoarchitecture. These findings allow us to design and tailor the optical and hydrophilic properties of the titania coatings.
Compositional and physico-optical characterization of 0–5% Al-doped zinc oxide films prepared by chemical spray pyrolysis
Authors: Romero R , López-Ibáñez R , Dalchiele E A , Ramos-Barrado J R , Martín F , Leinen D
Published: February 2010

Highly transparent polycrystalline Al-doped ZnO thin films were deposited in open atmosphere by chemical spray pyrolysis on fused silica and glass substrates at 623 K. The influence of Al doping, 0 to 5%, was studied. XPS results revealed a linear relationship between Al content in the precursor solutions and Al content in the films. XPS depth profiling showed that any carbon contamination is restricted to the uppermost surface of the films. Optical transmission measurements revealed an increasing number of dispersion centres as well as a band gap shift to higher values with increasing Al content in the films. At fixed Al concentration, the comparison of the absorption coefficient for increasing film thickness showed that the films are very homogeneous, not changing their materials properties such as absorption coefficient and band gap.
The effect of barrier layer-mediated catalytic deactivation in vertically aligned carbon nanotube growth
Authors: Patole S P , Yu Seong-Man , Shin Dong-Wook , Kim Ha-Jin , Han In-Taek , Kwon Kee-Won , Yoo Ji-Beom
Published: February 2010

The effect of Al-barrier layer-mediated Fe-catalytic deactivation in vertically aligned carbon nanotube (CNT) growth was studied. The substrate surface morphology, catalytic diffusion and barrier layer oxidation were found to be dependent on the annealing temperature of the barrier layer, which ultimately affects CNT growth. The annealed barrier layer without complete oxidation was found to be suitable for top to bottom super aligned CNT arrays. The highest average CNT growth rate of up to 3.88 µm s−1 was observed using this simple approach. Details of the analysis are also presented.
Superbroadband near-infrared emission from Cr–Ni co-doped transparent forsterite glass ceramics
Authors: Zhuang Yixi , Guan Miaojia , Xie Junhua , Teng Yu , Zhou Jiajia , Zhou Shifeng , Ruan Jian , Qiu Jianrong
Published: February 2010

Cr2O3 and NiO are co-doped in transparent forsterite glass ceramics. Absorption, emission spectra and fluorescence lifetime are performed to analyse the luminescence characteristics. Several near-infrared active centres are identified and energy transfer from Cr3+ and Cr4+ to Ni2+ is confirmed. Superbroadband near-infrared luminescence with a full width at half maximum of 700 nm is observed, which covers the whole telecommunication window.
Fabrication of nano-sized grains by pulsed laser surface melting
Authors: Wang Chengtao , Zhou Hong , lin Pengyu , Sun Na , Guo Qingchen , Yu Jiaxiang , Wang Mingxing , Zhao Yu , Ren Luquan
Published: February 2010

In this work, the formation and characterization of nano-sized grains on the modified surfaces of GCr15 and H13 steels have been investigated. The material was processed by pulsed laser surface melting (LSM) under different depths of de-ionized water. The microstructures and phases of the melted zones were examined by x-ray diffraction, environmental field emission scanning electron microscopy and high resolution transmission electron microscopy. The results indicate that LSM under water can successfully fabricate nano-scaled grains on the surfaces of steel, due to the rapid solidification and crystallization by heterogeneous nucleation. The elemental segregation of chromium and activated heterogeneous nucleation mechanism of austenite in liquid metal play a key role in the formation of nano-sized grains at high cooling rates. This one-step technique provides us a new way to prepare uniform nano-scaled grains, and is of great importance for further understanding the growth of nano-materials under extreme conditions.
Indentation-induced formation of low-dimensional Si structures in KOH solution
Authors: Yang Fuqian , Li Ding
Published: February 2010

Low-dimensional Si structures, including Si nanobelts and Si micropyramids, were formed on the surface of n-type silicon by microindentation and anisotropic etching in 30 wt% KOH solution at a temperature of 50 °C. The indentation was performed to create local plastic deformation and residual stresses. The residual stresses caused the formation of the Si nanobelts around the sites of indents on the surface of Si (1 1 1) and the Si micropyramids at the sites of indents on the surface of Si (1 0 0). The formation of the Si micropyramids was due to the local ‘mask’ created by the indentation and the residual stress around the indents. The residual hydrostatic stress at the tensile state increased the local etching rate, which resulted in a surface depression around the indents. The combination of indentation and wet etching process provides a maskless process to potentially produce low-dimensional Si structures in KOH solution at low temperatures.
A new emission inventory for nonagricultural open fires in Asia from 2000 to 2009
Authors: Song Yu , Chang Di , Liu Bing , Miao Weijie , Zhu Lei , Zhang Yuanhang
Published: February 2010

Open fires play a significant role in atmospheric pollution and climatic change. This work aims to develop an emission inventory for nonagricultural open fires in Asia using the newly released MODIS (Moderate Resolution Imaging Spectroradiometer) burned area product (MCD45A1), as the MODIS sensor cannot efficiently detect field crop residue burning. Country-level or province-specific biomass density data were used as fuel loads. Moisture contents were taken into account when calculating combustion factors for grass fuel. During the nine fire years 2000–2008, both burned areas and fire emissions clearly presented spatial and seasonal variations. Extensive nonagricultural open fires were concentrated in the months of February and March, while another peak was between August and October. Indonesia was the most important contributor to fire emission, which was largely attributable to peat burning. Myanmar, India, and Cambodia together contributed approximately half of the total burned area and emission. The annual emissions for CO2, CO, CH4, NMHCs, NOx, NH3, SO2, BC, OC, PM2.5, and PM10were 83 (69–103), 6.1 (4.6–8.2), 0.38 (0.24–0.57), 0.64 (0.36–1.0), 0.085 (0.074–0.10), 0.31 (0.17–0.48), 0.030 (0.024–0.037), 0.023 (0.020–0.028), 0.27 (0.22–0.33), 2.0 (1.6–2.6), and 2.2 (1.7–2.9) Tg yr− 1, respectively. This inventory has a daily temporal resolution and 500 m spatial resolution, and covers a long period, from April 2000 to February 2009. It could be used in global and regional air quality modeling.
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data
Authors: Hollunder Jens , Friedel Maik , Kuiper Martin , Wilhelm Thomas
Published: February 2010

Summary: Many large ‘omics’ datasets have been published and many more are expected in the near future. New analysis methods are needed for best exploitation. We have developed a graphical user interface (GUI) for easy data analysis. Our discovery of all significant substructures (DASS) approach elucidates the underlying modularity, a typical feature of complex biological data. It is related to biclustering and other data mining approaches. Importantly, DASS-GUI also allows handling of multi-sets and calculation of statistical significances. DASS-GUI contains tools for further analysis of the identified patterns: analysis of the pattern hierarchy, enrichment analysis, module validation, analysis of additional numerical data, easy handling of synonymous names, clustering, filtering and merging. Different export options allow easy usage of additional tools such as Cytoscape.

Availability: Source code, pre-compiled binaries for different systems, a comprehensive tutorial, case studies and many additional datasets are freely available at http://www.ifr.ac.uk/dass/gui/. DASS-GUI is implemented in Qt.

Contact:  jehol@psb.vib-ugent.be; thomas.wilhelm@bbsrc.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1
Authors: Natale Massimo , Bonino Dario , Consoli Paolo , Alberio Tiziana , Ravid Rivka G. , Fasano Mauro , Bucci Enrico M.
Published: February 2010

Motivation: The two-dimensional electrophoresis (2-DE) pattern of proteins is thought to be specifically related to the physiological or pathological condition at the moment of sample preparation. On this ground, most proteomic studies move to identify specific hallmarks for a number of different conditions. However, the information arising from these investigations is often incomplete due to inherent limitations of the technique, to extensive protein post-translational modifications and sometimes to the paucity of available samples.

The meta-analysis of proteomic data can provide valuable information pertinent to various biological processes that otherwise remains hidden.

Results: Here, we show a meta-analysis of the PD protein DJ-1 in heterogeneous 2-DE experiments. The protein was shown to segregate into specific clusters associated with defined conditions.

Interestingly, the DJ-1 pool from neural tissues displayed a specific and characteristic molecular weight and isoelectric point pattern. Moreover, changes in this pattern have been related to neurodegenerative processes and aging. These results were experimentally validated on human brain specimens from control subjects and PD patients.

Availability: ImageJ is a public domain image processing program developed by the National Institutes of Health and is freely available at http://rsbweb.nih.gov/ij. All the ImageJ macros used in this study are available as supplementary material and upon request at info@biodigitalvalley.com. XLSTAT can be purchased online at http://www.xlstat.com/en/home/ at a current cost of ∼300 EUR.

Contact:  enrico.bucci@biodigitalvalley.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Administration of Chinpi, a Component of the Herbal Medicine Ninjin‐Youei‐To, Reverses Age‐Induced Demyelination
Authors: Sato Nanako , Seiwa Chika , Uruse Michihiro , Yamamoto Masahiro , Tanaka Kayoko , Kawakita Takuya , Komatsu Yasuhiro , Yasukawa Akio , Takao Masakatsu , Kudo Chiaki , Hasegawa Atsuhiko , Ishige Atushi , Watanabe Kenji , Asou Hiroaki
Published: February 2010

The disruption of myelin causes severe neurological diseases. An understanding of the mechanism of myelination and remyelination is essential for the development of therapeutic strategies for demyelination diseases. Our previous findings indicated that the FcRγ/Fyn cascade is a potential therapeutic target for remyelination caused by the Chinese/Japanese traditional herbal (Kampo) medicine ninjin’youeito (Ninjin‐youei‐to, NYT), which is a hot‐water extract made from 12 medicinal herbs. To identify which constituents of NYT are involved in the reversal of demyelination and to examine the potential therapeutic effect, we tested several of the chemical constituents of NYT. Here, we report that Chinpi, a constituent of NYT, upregulates the FcRγ/Fyn signaling cascade resulting in a potentially therapeutic effect against age‐induced demyelination. In addition, we observed that phosphorylated (activated) FcRγ/Fyn upregulated the expression of the 21.5 kDa isoform of myelin basic protein, inducing rapid morphological differentiation, when oligodendrocyte precursor cells (OPCs) were cultured in the presence of hesperidin and/or narirutin (the major active constituents of Chinpi). These results suggest that hesperidin and narirutin participate in the FcRγ/Fyn signaling pathway in OPCs causing these cells to differentiate into myelinating oligodendrocytes.
Is Sham Laser a Valid Control for Acupuncture Trials?
Authors: Irnich Dominik , Salih Norbert , Offenbächer Martin , Fleckenstein Johannes
Published: February 2010

Methodological problems of acupuncture trials focus on adequate placebo controls. In this trial we evaluated the use of sham laser acupuncture as a control procedure. Thirty‐four healthy volunteers received verum laser (invisible infrared laser emission and red light, 45 s and 1 J per point) and sham laser (red light) treatment at three acupuncture points (LI4, LU7 and LR3) in a randomized, double‐blinded, cross‐over design. The main outcome measure was the ratio of correct to incorrect ratings of treatment immediately after each session. The secondary outcome measure was the occurrence of deqi‐like sensations at the acupuncture points and their intensity on a 10‐fold visual analog scale (VAS; 10 being the strongest sensible sensation). We pooled the results of three former trials to evaluate the credibility of sham laser acupuncture when compared to needle acupuncture. Fifteen out of 34 (44%) healthy volunteers (age: 28 ± 10.7 years) identified the used laser device after the first session and 14 (41%) after the second session. Hence, both treatments were undistinguishable (P = .26). Deqi‐like sensations occurred in 46% of active laser (2.34 VAS) and in 49.0% of sham laser beams (2.49 VAS). The credibility of sham laser was not different from needle acupuncture. Sham laser acupuncture can serve as a valid placebo control in laser acupuncture studies. Due to similar credibility and the lack of sensory input on the peripheral nervous system, sham laser acupuncture can also serve as a sham control for acupuncture trials, in order to evaluate needling effects per se.
Methylglyoxal—A Potential Risk Factor of Manuka Honey in Healing of Diabetic Ulcers
Authors: Majtan Juraj
Published: February 2010

Honey has been considered as a remedy in wound healing since ancient times. However, as yet, there are inadequate supportive robust randomized trials and experimental data to fully accept honey as an effective medical product in wound care. Manuka honey has been claimed to have therapeutic advantages over other honeys. Recently, it has been documented that the pronounced antibacterial activity of manuka honey is due, at least in part, to reactive methylglyoxal (MG). The concentration of MG in manuka honeys is up to 100‐fold higher than in conventional honeys. MG is a potent protein‐glycating agent and an important precursor of advanced glycation end products (AGEs). MG and AGEs play a role in the pathogenesis of impaired diabetic wound healing and can modify the structure and function of target molecules. This commentary describes the concern that MG in manuka honey may delay wound healing in diabetic patients. Further detailed research is needed to fully elucidate the participation of honey/derived MG in healing diabetic ulcers. We advocate randomized controlled trials to determine efficacy and safety of manuka honey in this population.
Adherence to the medical regime in patients with heart failure
Authors: Muzzarelli Stefano , Brunner‐La Rocca Hanspeter , Pfister Otmar , Foglia Pietro , Moschovitis Giorgio , Mombelli Giorgio , Stricker Hans
Published: February 2010

Aims

To assess adherence to medical treatment in patients with heart failure (HF) using a specific questionnaire and measurement of the serum concentration of digoxin.

Methods and results

Forty patients with symptomatic HF and a clinical indication for digoxin were included in this pilot study. The assessment of adherence to the medical regime was based on two different methods: (i) the CARDIA‐Questionnaire and (ii) the measurement of serum digoxin concentration (SDC) at 1 and 6 months. All patients were placed on digoxin treatment (target SDC 0.6–0.8 ng/mL) at baseline. Poor adherence was defined if the patient self‐reported taking ≤75% of the prescribed HF medication or had an SDC < 0.4 ng/mL (subtherapeutic range) at the follow‐up visits. During the entire follow‐up, the proportion of patients with poor adherence was 15% as assessed by the questionnaire, 20% as assessed by the SDC, and 25% if both methods were combined.

Conclusion

Although HF is a symptomatic disease, the proportion of patients with poor adherence to the medical regime in our study was high (up to 25%). The objective methodology based on the measurement of the SDC identified a higher number of patients with poor adherence when compared with the CARDIA‐Questionnaire.
Thiomonas islandica sp. nov., a moderately thermophilic, hydrogen- and sulfur-oxidizing betaproteobacterium isolated from a hot spring
Authors: Vésteinsdóttir Hildur , Reynisdóttir Dagný B. , Örlygsson Johann
Published: February 2010

A novel, hydrogen- and sulfur-oxidizing bacterium, designated strain 6CT, was isolated from a hot spring in Graendalur, south-western Iceland. Cells of this organism were Gram-reaction-negative, rod-shaped and motile. The strain grew aerobically and was capable of chemolithotrophic growth on thiosulfate and hydrogen, heterotrophic growth on pyruvate, oxalate, acetate and on glutamate in the presence of yeast extract and mixotrophic growth on several organic compounds, thiosulfate and/or hydrogen. During growth on thiosulfate, the final product was sulfate, resulting in a drop in pH from 6.8 to 2.7. Heterotrophic growth on pyruvate was observed at pH 4–7 (optimum pH 4) and 35–50 °C (optimum 45 °C). The DNA G+C content was 65.2 mol%. As determined by 16S rRNA gene sequence analysis, strain 6CT represents a distinct species belonging to the class Betaproteobacteria and is most closely related to Thiomonas intermedia DSM 18155T and Thiomonas perometabolis DSM 18570T. DNA–DNA hybridization between strain 6CT and Thiomonas intermedia DSM 18155T and Thiomonas perometabolis DSM 18570T gave relatedness values below 32 %. These results, together with physiological characteristics, showed that strain 6CT represents a novel species within the genus Thiomonas, for which the name Thiomonas islandica sp. nov. is proposed. The type strain is 6CT (=DSM 21436T =JCM 16107T).
Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil
Authors: Rezgui Raja , Ben Ali Gam Zouhaier , Ben Hamed Said , Fardeau Marie-Laure , Cayol Jean-Luc , Maaroufi Abderrazak , Labat Marc
Published: February 2010

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37T, was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37T stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37T had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C15 : 0 (41 %), iso-C14 : 0 3-OH and/or iso-C15 : 0 dimethyl acetal (21.6 %), iso-C13 : 0 (4.4 %), anteiso-C15 : 0 (3.9 %) and iso-C15 : 1 (2.8 %). Strain SOL3f37T grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2–8.1 (optimum pH 6.9). Strain SOL3f37T required at least 0.5 g NaCl l−1 and grew in the presence of NaCl concentrations up to 150 g l−1 (optimum 40 g l−1). Yeast extract (2 g l−1) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37T grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37T was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37T was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60T, 91.8 % with Thermohalobacter berrensis CTT3T and 91.7 % with Caloranaerobacter azorensis MV1087T. On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37T represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is proposed, with SOL3f37T (=DSM 21485T =JCM 15487T) as the type strain of Sporosalibacterium faouarense.
Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring
Authors: Dubinina Galina , Grabovich Margarita , Leshcheva Natalia , Rainey Frederick A. , Gavrish Ekaterina
Published: February 2010

A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated PTwas isolated from a sulfur ‘Thiodendron’ mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain PTexhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H2O2with sulfide and deposit it in the periplasmic space. Growth occurred at 4–32 °C (optimum at 28–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5), and in 0.1–1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO2and H2. The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain PTfell within a group of species in the genusSpirochaeta, includingSpirochaeta litoralis,S. isovalericaandS. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genusSpirochaeta, for which the nameSpirochaeta perfilieviisp. nov. is proposed. The type strain is PT(=DSM 19205T=VKM B-2514T).
Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae
Authors: Kim Sun-Jung , Lee Sang-Seob
Published: February 2010

A Gram-positive, non-motile bacterium, designated KSL51201-037T, was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037T belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17T, 96.0 % to Leifsonia ginsengi wged11T and 95.9 % to Microterricola viridarii KV-677T. The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037T had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C15 : 0 (47.8 %) and iso-C16 : 0 (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037T represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037T (=KEMC 51201-037T=JCM 16463T).
Streptomyces lacticiproducens sp. nov., a lactic acid-producing streptomycete isolated from the rhizosphere of tomato plants
Authors: Zhu Hong-Hui , Yao Qing , Yang Song-Zhen , Li Zhi-Kun , Guo Jun
Published: February 2010

A novel actinomycete, designated strain GIMN4.001T, was isolated from the rhizosphere of tomato plants grown in Guangzhou, China. The strain produced greyish white aerial mycelia, lactic acid and a large quantity of double diamond-shaped crystals on potato dextrose agar and yeast extract-malt extract agar. The colour of the substrate mycelium was not sensitive to pH. Microscopic observations revealed that strain GIMN4.001T produced verticillate chains of cylindrical spores. Chemotaxonomic data confirmed that strain GIMN4.001T belonged to the genus Streptomyces. Melanin pigments were not produced. No antibacterial activity was observed against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis or Candida albicans, but inhibitory activity was observed against Penicillium citrinum. 16S rRNA gene sequence analysis revealed that strain GIMN4.001T was related most closely to Streptomyces morookaense ATCC 19166T (98.9 % similarity) and Streptomyces lavenduligriseus ATCC 13306T (98.7 %). Levels of DNA–DNA relatedness between strain GIMN4.001T and the type strains of these species were low (14–20 %). Furthermore, strain GIMN4.001T could be differentiated from S. morookaense, S. lavenduligriseus and other closely related species of the genus Streptomyces based on morphological, physiological and biochemical characteristics. On the basis of its physiological and molecular properties, strain GIMN4.001T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lacticiproducens sp. nov. is proposed. The type strain is GIMN4.001T (=CCTCC M208214T=NRRL B-24800T).
Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs
Authors: Zhang Chun-Mei , Huang Xiao-Wei , Pan Wen-Zheng , Zhang Jing , Wei Kang-Bi , Klenk Hans-Peter , Tang Shu-Kun , Li Wen-Jun , Zhang Ke-qin
Published: February 2010

Two novel thermophilic, spore-forming bacterial strains, T-11T and E-112T, were isolated from hot springs in Tengchong and Eryuan counties of Yunnan province in south-west China. The strains were Gram-stain-positive rods, occurring singly or in chains. Growth of strain T-11T was observed between 30 and 75 °C (optimum 50 °C) and at pH 7–11 (optimum pH 8.5), while the temperature range for strain E-112T was 35–70 °C (optimum 55 °C) and the pH range was 7.0–11.0 (optimum pH 8.0). The DNA G+C contents of strains T-11T and E-112T were 41.1 and 42.6 mol%, respectively. On the basis of 16S rRNA gene sequence similarity, the two strains were shown to be related most closely to Anoxybacillus species. The chemotaxonomic characteristics [predominant isoprenoid quinone menaquinone 7 (MK-7); major fatty acids iso-C15 : 0 and iso-C17 : 0] also supported the affiliation of strains T-11T and E-112T to the genus Anoxybacillus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains T-11T and E-112T from Anoxybacillus species with validly published names. Strains T-11T and E-112T therefore represent two novel species, for which the names Anoxybacillus tengchongensis sp. nov. (type strain T-11T =CCTCC AB209237T =KCTC 13721T) and Anoxybacillus eryuanensis sp. nov. (type strain E-112T =CCTCC AB209236T =KCTC 13720T) are proposed.
Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost
Authors: Shcherbakova Viktoria , Rivkina Elizaveta , Pecheritsyna Svetlana , Laurinavichius Kestus , Suzina Nataliya , Gilichinsky David
Published: February 2010

A mesophilic, non-motile, hydrogenotrophic, rod-shaped methanogen, designated M2T, was isolated from Holocene permafrost sediments of the Kolyma lowland in the Russian Arctic. Cells were 3–6 μm long and 0.45–0.5 μm wide. Strain M2T grew on H2/CO2 and formate. Optimum conditions for growth were 37 °C, pH 6.8–7.2 and 0.1 M NaCl. The DNA G+C content was 38.1 mol%. On the basis of 16S rRNA gene sequence comparison with known methanogens, strain M2T was affiliated with the genus Methanobacterium and was most closely related to Methanobacterium veterum MK4T and Methanobacterium bryantii DSM 863T (both 99 % 16S rRNA gene sequence similarity). However, no significant DNA–DNA relatedness was observed between strain M2T and these type strains. We propose that strain M2T represents a novel species, with the name Methanobacterium arcticum sp. nov., with type strain M2T (=DSM 19844T =VKM B-2371T).
Neisseria wadsworthii sp. nov. and Neisseria shayeganii sp. nov., isolated from clinical specimens
Authors: Wolfgang William J. , Carpenter Andrea N. , Cole Jocelyn A. , Gronow Sabine , Habura Andrea , Jose Sherly , Nazarian Elizabeth J. , Kohlerschmidt Donna J. , Limberger Ronald , Schoonmaker-Bopp Dianna , Spröer Cathrin , Musser Kimberlee A.
Published: February 2010

An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species. For each species, two strains from independent sources were identified. Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri. DNA–DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours. Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation. Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis. The predominant cellular fatty acids [16 : 0, summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) and 18 : 1ω7c], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov. (type strain 9715T =DSM 22247T =CIP 109934T) and Neisseria shayeganii sp. nov. (type strain 871T =DSM 22246T =CIP 109933T).
Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments
Authors: Mori Koji , Harayama Shigeaki
Published: February 2010

Two methane-producing archaea, designated Mic5c12T and Mic6c05T, were isolated from sludge deposited in a crude oil storage tank and a tubercle on the interior of a pipe transporting natural gas-containing brine, respectively. The isolates were Gram-staining-variable, non-motile rods and grew only on H2/CO2. Strain Mic6c05T produced methane from some alcohols without showing any growth; strain Mic5c12T did not utilize alcohols. The optimum growth conditions for strain Mic5c12T were 35 °C, pH 6.5 and 0–0.68 M NaCl and for strain Mic6c05T were 40 °C, pH 6.0–7.5 and 0.34 M NaCl. Strain Mic5c12T was halotolerant and strain Mic6c05T was halophilic. Comparative 16S rRNA gene sequence analysis revealed that strains Mic5c12T and Mic6c05T belonged to the genus Methanobacterium and their closest relative was Methanobacterium subterraneum A8pT (97.3 and 97.9 % 16S rRNA gene sequence similarity, respectively). The findings from the 16S rRNA gene sequence analyses were supported by analysis of McrA, the alpha subunit of methyl-coenzyme M reductase. On the basis of phylogenetic analyses and phenotypic characteristics, two novel species are proposed, Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., with type strains Mic5c12T (=NBRC 105198T =DSM 22353T) and Mic6c05T (=NBRC 105197T =DSM 21974T), respectively.
Tracing Cadmium from Culture to Spikelet: Noninvasive Imaging and Quantitative Characterization of Absorption, Transport, and Accumulation of Cadmium in an Intact Rice Plant
Authors: Fujimaki Shu , Suzui Nobuo , Ishioka Noriko S. , Kawachi Naoki , Ito Sayuri , Chino Mitsuo , Nakamura Shin-ichi
Published: February 2010

We characterized the absorption and short-term translocation of cadmium (Cd) in rice (Oryza sativa ‘Nipponbare’) quantitatively using serial images observed with a positron-emitting tracer imaging system. We fed a positron-emitting 107Cd (half-life of 6.5 h) tracer to the hydroponic culture solution and noninvasively obtained serial images of Cd distribution in intact rice plants at the vegetative stage and at the grain-filling stage every 4 min for 36 h. The rates of absorption of Cd by the root were proportional to Cd concentrations in the culture solution within the tested range of 0.05 to 100 nm. It was estimated that the radial transport from the culture to the xylem in the root tissue was completed in less than 10 min. Cd moved up through the shoot organs with velocities of a few centimeters per hour at both stages, which was obviously slower than the bulk flow in the xylem. Finally, Cd arrived at the panicles 7 h after feeding and accumulated there constantly, although no Cd was observed in the leaf blades within the initial 36 h. The nodes exhibited the most intensive Cd accumulation in the shoot at both stages, and Cd transport from the basal nodes to crown root tips was observed at the vegetative stage. We conclude that the nodes are the central organ where xylem-to-phloem transfer takes place and play a pivotal role in the half-day travel of Cd from the soil to the grains at the grain-filling stage.
Nonhost Resistance of Barley to Different Fungal Pathogens Is Associated with Largely Distinct, Quantitative Transcriptional Responses
Authors: Zellerhoff Nina , Himmelbach Axel , Dong Wubei , Bieri Stephane , Schaffrath Ulrich , Schweizer Patrick
Published: February 2010

Nonhost resistance protects plants against attack by the vast majority of potential pathogens, including phytopathogenic fungi. Despite its high biological importance, the molecular architecture of nonhost resistance has remained largely unexplored. Here, we describe the transcriptional responses of one particular genotype of barley (Hordeum vulgare subsp. vulgare ‘Ingrid’) to three different pairs of adapted (host) and nonadapted (nonhost) isolates of fungal pathogens, which belong to the genera Blumeria (powdery mildew), Puccinia (rust), and Magnaporthe (blast). Nonhost resistance against each of these pathogens was associated with changes in transcript abundance of distinct sets of nonhost-specific genes, although general (not nonhost-associated) transcriptional responses to the different pathogens overlapped considerably. The powdery mildew- and blast-induced differences in transcript abundance between host and nonhost interactions were significantly correlated with differences between a near-isogenic pair of barley lines that carry either the Mlo wild-type allele or the mutated mlo5 allele, which mediates basal resistance to powdery mildew. Moreover, during the interactions of barley with the different host or nonhost pathogens, similar patterns of overrepresented and underrepresented functional categories of genes were found. The results suggest that nonhost resistance and basal host defense of barley are functionally related and that nonhost resistance to different fungal pathogens is associated with more robust regulation of complex but largely nonoverlapping sets of pathogen-responsive genes involved in similar metabolic or signaling pathways.