bluuebunny/crossref_metadata_2025 huggingface dataset:
CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in
Arabidopsis
Authors: Dong Malia A. , Farré Eva M. , Thomashow Michael F.
Published: April 2011

The C-REPEAT BINDING FACTOR (CBF) cold-response pathway has a prominent role in cold acclimation, the process whereby certain plants increase tolerance to freezing in response to low nonfreezing temperatures. In
Arabidopsis
, the CBF pathway is characterized by rapid induction of the
C-REPEAT BINDING FACTOR 1
(
CBF1
),
CBF2
, and
CBF3
genes, which encode transcriptional activators, followed by induction of the CBF-targeted genes known as the “CBF regulon.” Expression of the CBF regulon results in an increase in freezing tolerance. Previous studies established that
CBF1, CBF2
, and
CBF3
are subject to circadian regulation and that their cold induction is gated by the circadian clock. Here we present the results of genetic analysis and ChIP experiments indicating that both these forms of regulation involve direct positive action of two transcription factors that are core components of the clock, i.e., CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). In plants carrying the
cca1
-11/
lhy
-21 double mutation, cold induction of
CBF1
,
CBF2
, and
CBF3
was greatly impaired, and circadian regulation of
CBF1
and
CBF3
was essentially eliminated; circadian regulation of
CBF2
continued, although with significantly reduced amplitude. Circadian regulation and cold induction of three CBF regulon genes, i.e.,
COLD-REGULATED GENE15A
(
COR15A
),
COR47
, and
COR78
, also were greatly diminished in plants carrying the
cca1
-11/
lhy
-21 double mutation. Furthermore, the
cca1
-11/
lhy
-21 double mutation resulted in impaired freezing tolerance in both nonacclimated and cold-acclimated plants. These results indicate that CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway.
Photocatalytic activity of La–N-codoped NaTaO3 for H2 evolution from water under visible-light irradiation
Authors: Zhao Zongyan , Li Ruipu , Li Zhaosheng , Zou Zhigang
Published: April 2011

A La–N-codoped NaTaO3 photocatalyst was synthesized by the solid-state reaction and thermal ammonolysis method. The photocatalytic reactions showed that La–N-codoped NaTaO3 has high activity of H2 evolution (7.0 µmol h−1) and long time stability under visible-light irradiation (λ > 420 nm). DFT calculations suggested that the visible-light absorption of La–N-codoped NaTaO3 originated from the transition of electrons from the impurity states to the bottom of the conduction band.
Synthesis and photoluminescence of CdS QDs in ZrO2 nanotubes by sequential chemical bath deposition
Authors: Guo Limin , Wang Xiaohui , Zhong Caifu , Li Longtu
Published: April 2011

Highly ordered ZrO2 nanotube (NT) arrays were fabricated by anodization in organic electrolyte containing NH4F. A facile sequential-chemical bath deposition technique was used to prepare CdS quantum dots (QDs) in the pores of ZrO2 NTs. XRD and HRTEM results confirmed the formation of single-phase wurtzite CdS nanoparticles with uniform size around 10 nm. UV–vis absorption and photoluminescence spectra proved that the CdS QD coating strongly enhanced the photon absorption of the NT arrays, as well as their PL signals in the visible broadband section which mostly arose from structure-dependent defects and oxygen vacancies in the nanohybrid layers.
Rapid compression preparation and characterization of oversized bulk amorphous polyether-ether-ketone
Authors: Yuan C S , Hong S M , Li X X , Shen R , He Z , Lv S J , Liu X R , Lv J , Xi D K
Published: April 2011

Melts of polyether-ether-ketone (PEEK) with three kinds of average molecular weight are solidified by rapid compression from 0.1 to 2.0 GPa at 360 °C within 20 ms, and comparative samples are also made by rapid quenching and slow cooling of the same melts. Through XRD and DSC analyses and mechanical tests of the recovered samples, it is found that bulk materials of PEEK obtained by rapid compression exhibit a single amorphous phase with unique properties such as high thermodynamic stability, excellent friction and wear behaviour, considerable stiffness, exceptional ductile character and high impact toughness. These properties could be attributed to their homogeneous fine structure. A bulk and fully amorphous PEEK with 24 mm diameter and 12 mm thickness is prepared by rapid compression, which considerably exceeds the critical size in a conventional quenching method, thus, directly confirming that the size of the amorphous material is not limited by thermal conductivity in the rapid compression process.
Multifunctional dual-tunable multiferroic Ba0.25Sr0.75TiO3–BiFeO3–Ba0.25Sr0.75TiO3 trilayered structure for tunable microwave applications
Authors: Sheng Su , Ong C K
Published: April 2011

A multiferroic trilayered structure composed of a BiFeO3 (BFO) layer and two Ba0.25Sr0.75TiO3 (BST) layers is grown on a Pt/TiO2/SiO2/Si substrate by pulsed laser deposition. The trilayered BST/BFO/BST thin film structure exhibits a significant tuning response for the dielectric constant with an electric field and a magnetic field, respectively. Microwave devices based on such multifunctional materials can offer dual, i.e. electric and magnetic, tuning possibility and extra flexibility in designing and shaping the device performances.
Depth of edge rings arising from finite graphs
Authors: Hibi Takayuki , Higashitani Akihiro , Kimura Kyouko , O’Keefe Augustine
Published: April 2011

Let

G
G

be a finite graph and

K
[
G
]

K[G]

the edge ring of

G
G

. Based on the technique of Gröbner bases and initial ideals, it will be proved that, given integers

f
f

and

d
d

with

7
≤
f
≤
d

7 \leq f \leq d

, there exists a finite graph

G
G

on

[
d
]
=
{
1
,
…
,
d
}

[d] = \{ 1, \ldots , d \}

with

depth

K
[
G
]
=
f

\textrm {depth}\, K[G] = f

and with

Krull-dim

K
[
G
]
=
d

\textrm {Krull-dim}\, K[G] = d

.
In neurons, activity-dependent association of dendritically transported mRNA transcripts with the transacting factor CBF-A is mediated by A2RE/RTS elements
Authors: Raju Chandrasekhar S. , Fukuda Nanaho , López-Iglesias Carmen , Göritz Christian , Visa Neus , Percipalle Piergiorgio
Published: April 2011

In neurons certain mRNA transcripts are transported to synapses through mechanisms that are not fully understood. Here we report that the heterogeneous nuclear ribonucleoprotein CBF-A (CArG Box binding Factor A) facilitates dendritic transport and localization of activity-regulated cytoskeleton-associated protein (Arc), brain-derived neurotrophic factor (BDNF), and calmodulin-dependent protein kinase II (CaMKIIα) mRNAs. We discovered that, in the adult mouse brain, CBF-A has a broad distribution. In the nucleus, CBF-A was found at active transcription sites and interchromosomal spaces and close to nuclear pores. In the cytoplasm, CBF-A localized to dendrites as well as pre- and postsynaptic sites. CBF-A was found in synaptosomal fractions, associated with Arc, BDNF, and CaMKIIα mRNAs. Electrophoretic mobility shift assays demonstrated a direct interaction mediated via their hnRNP A2 response element (A2RE)/RNA trafficking sequence (RTS) elements located in the 3′ untranslated regions. In situ hybridization and microscopy on live hippocampal neurons showed that CBF-A is in dynamic granules containing Arc, BDNF, and CaMKIIα mRNAs. N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) postsynaptic receptor stimulation led to CBF-A accumulation in dendrites; increased Arc, BDNF, and CaMKIIα mRNA levels; and increased amounts of transcripts coprecipitating with CBF-A. Finally, CBF-A gene knockdown led to decreased mRNA levels. We propose that CBF-A cotranscriptionally binds RTSs in Arc, BDNF, and CaMKIIα mRNAs and follows the transcripts from genes to dendrites, promoting activity-dependent nuclear sorting of transport-competent mRNAs.
Tyrosine phosphorylation–dependent activation of TRPC6 regulated by PLC-γ1 and nephrin: effect of mutations associated with focal segmental glomerulosclerosis
Authors: Kanda Shoichiro , Harita Yutaka , Shibagaki Yoshio , Sekine Takashi , Igarashi Takashi , Inoue Takafumi , Hattori Seisuke
Published: April 2011

Transient receptor potential canonicals (TRPCs) play important roles in the regulation of intracellular calcium concentration. Mutations in the TRPC6 gene are found in patients with focal segmental glomerulosclerosis (FSGS), a proteinuric disease characterized by dysregulated function of renal glomerular epithelial cells (podocytes). There is as yet no clear picture for the activation mechanism of TRPC6 at the molecular basis, however, and the association between its channel activity and pathogenesis remains unclear. We demonstrate here that tyrosine phosphorylation of TRPC6 induces a complex formation with phospholipase C (PLC)-γ1, which is prerequisite for TRPC6 surface expression. Furthermore, nephrin, an adhesion protein between the foot processes of podocytes, binds to phosphorylated TRPC6 via its cytoplasmic domain, competitively inhibiting TRPC6–PLC-γ1 complex formation, TRPC6 surface localization, and TRPC6 activation. Importantly, FSGS-associated mutations render the mutated TRPC6s insensitive to nephrin suppression, thereby promoting their surface expression and channel activation. These results delineate the mechanism of TRPC6 activation regulated by tyrosine phosphorylation, and imply the cell type–specific regulation, which correlates the FSGS mutations with deregulated TRPC6 channel activity.
Nuclear localization of the meiosis-specific transcription factor Ndt80 is regulated by the pachytene checkpoint
Authors: Wang Ying , Chang Chun-Yu , Wu Jing-Fen , Tung Kuei-Shu
Published: April 2011

In budding yeast, the Ndt80 protein is a meiosis-specific transcription factor that is essential for the exit of pachytene and progression into nuclear divisions and spore formation. The pachytene checkpoint responds to defects in meiotic recombination and chromosome synapsis and negatively regulates the activity of Ndt80. The activity of Ndt80 was suggested to be regulated at both transcriptional and posttranslational levels; however, the mechanism for posttranslational regulation of Ndt80 was unclear. From a study of ndt80 in-frame deletion mutations, we have identified a dominant mutation NDT80-bc, which is able to completely bypass the pachytene checkpoint. The NDT80-bc mutation relieves the checkpoint-mediated arrest of the zip1, dmc1, and hop2 mutants, producing spores with low viability. The NDT80-bc mutant provides direct evidence for the posttranslational control of Ndt80 activity. Furthermore, the data presented show that Ndt80 is retained in cytoplasm in the zip1 mutant, whereas Ndt80-bc is found in the nucleus. We propose that the nuclear localization of Ndt80 is regulated by the pachytene checkpoint through a cytoplasmic anchor mechanism.
Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets
Authors: Bader Kai Christian , Grothoff Christian , Meier Harald
Published: April 2011

Motivation: PCR, hybridization, DNA sequencing and other important methods in molecular diagnostics rely on both sequence-specific and sequence group-specific oligonucleotide primers and probes. Their design depends on the identification of oligonucleotide signatures in whole genome or marker gene sequences. Although genome and gene databases are generally available and regularly updated, collections of valuable signatures are rare. Even for single requests, the search for signatures becomes computationally expensive when working with large collections of target (and non-target) sequences. Moreover, with growing dataset sizes, the chance of finding exact group-matching signatures decreases, necessitating the application of relaxed search methods. The resultant substantial increase in complexity is exacerbated by the dearth of algorithms able to solve these problems efficiently.

Results: We have developed CaSSiS, a fast and scalable method for computing comprehensive collections of sequence- and sequence group-specific oligonucleotide signatures from large sets of hierarchically clustered nucleic acid sequence data. Based on the ARB Positional Tree (PT-)Server and a newly developed BGRT data structure, CaSSiS not only determines sequence-specific signatures and perfect group-covering signatures for every node within the cluster (i.e. target groups), but also signatures with maximal group coverage (sensitivity) within a user-defined range of non-target hits (specificity) for groups lacking a perfect common signature. An upper limit of tolerated mismatches within the target group, as well as the minimum number of mismatches with non-target sequences, can be predefined. Test runs with one of the largest phylogenetic gene sequence datasets available indicate good runtime and memory performance, and in silico spot tests have shown the usefulness of the resulting signature sequences as blueprints for group-specific oligonucleotide probes.

Availability: Software and Supplementary Material are available at http://cassis.in.tum.de/.

Contact:  meierh@in.tum.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
ProDy: Protein Dynamics Inferred from Theory and Experiments
Authors: Bakan Ahmet , Meireles Lidio M. , Bahar Ivet
Published: April 2011

Summary: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods.

Availability:  ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.

Contact:  ahb12@pitt.edu; bahar@pitt.edu
Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
Authors: Teschendorff Andrew E. , Zhuang Joanna , Widschwendter Martin
Published: April 2011

Motivation: A common difficulty in large-scale microarray studies is the presence of confounding factors, which may significantly skew estimates of statistical significance, cause unreliable feature selection and high false negative rates. To deal with these difficulties, an algorithmic framework known as Surrogate Variable Analysis (SVA) was recently proposed.

Results: Based on the notion that data can be viewed as an interference pattern, reflecting the superposition of independent effects and random noise, we present a modified SVA, called Independent Surrogate Variable Analysis (ISVA), to identify features correlating with a phenotype of interest in the presence of potential confounding factors. Using simulated data, we show that ISVA performs well in identifying confounders as well as outperforming methods which do not adjust for confounding. Using four large-scale Illumina Infinium DNA methylation datasets subject to low signal to noise ratios and substantial confounding by beadchip effects and variable bisulfite conversion efficiency, we show that ISVA improves the identifiability of confounders and that this enables a framework for feature selection that is more robust to model misspecification and heterogeneous phenotypes. Finally, we demonstrate similar improvements of ISVA across four mRNA expression datasets. Thus, ISVA should be useful as a feature selection tool in studies that are subject to confounding.

Availability: An R-package isva is available from www.cran.r-project.org.

Contact:  a.teschendorff@ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Phytobacterial Type III Effectors HopX1, HopAB1 and HopF2 Enhance Sense-Post-Transcriptional Gene Silencing Independently of Plant R Gene-Effector Recognition
Authors: Sarris Panagiotis F. , Gao Shang , Karademiris Konstantinos , Jin Hailing , Kalantidis Kriton , Panopoulos Nickolas J.
Published: April 2011

Plant- and animal-pathogenic bacteria deploy a variable arsenal of type III effector proteins (T3EP) to manipulate host defense. Specific biochemical functions and molecular or subcellular targets have been demonstrated or proposed for a growing number of T3EP but remain unknown for the majority of them. Here, we show that transient expression of genes coding certain bacterial T3EP (HopAB1, HopX1, and HopF2), which did not elicit hypersensitive response (HR) in transgenic green fluorescent protein (GFP) Nicotiana benthamiana 16C line, enhanced the sense post-transcriptional gene silencing (S-PTGS) triggered by agrodelivery of a GFP-expressing cassette and the silencing enhancement could be blocked by two well-known viral silencing suppressors. Further analysis using genetic truncations and site-directed mutations showed that the receptor recognition domains of HopAB1 and HopX1 are not involved in enhancing silencing. Our studies provide new evidence that phytobacterial pathogen T3EP manipulate the plant small interfering RNA pathways by enhancing silencing efficiency in the absence of effector-triggered immunity signaling and suggest that phytopathogenic bacterial effectors affect host RNA silencing in yet other ways than previously described.
Pectobacterium carotovorumElicits Plant Cell Death with DspE/F but theP. carotovorumDspE Does Not Suppress Callose or Induce Expression of Plant Genes Early in Plant–Microbe Interactions
Authors: Kim Hye-Sook , Thammarat Phanit , Lommel Steven A. , Hogan Clifford S. , Charkowski Amy O.
Published: April 2011

The broad-host-range bacterial soft rot pathogen Pectobacterium carotovorum causes a DspE/F-dependent plant cell death on Nicotiana benthamiana within 24 h postinoculation (hpi) followed by leaf maceration within 48 hpi. P. carotovorum strains with mutations in type III secretion system (T3SS) regulatory and structural genes, including the dspE/F operon, did not cause hypersensitive response (HR)-like cell death and or leaf maceration. A strain with a mutation in the type II secretion system caused HR-like plant cell death but no maceration. P. carotovorum was unable to impede callose deposition in N. benthamiana leaves, suggesting that P. carotovorum does not suppress this basal immunity function. Within 24 hpi, there was callose deposition along leaf veins and examination showed that the pathogen cells were localized along the veins. To further examine HR-like plant cell death induced by P. carotovorum, gene expression profiles in N. benthamiana leaves inoculated with wild-type and mutant P. carotovorum and Pseudomonas syringae strains were compared. The N. benthamiana gene expression profile of leaves infiltrated with Pectobacterium carotovorum was similar to leaves infiltrated with a Pseudomonas syringae T3SS mutant. These data support a model where Pectobacterium carotovorum uses the T3SS to induce plant cell death in order to promote leaf maceration rather than to suppress plant immunity.
Identification and Characterization of Botryosphaeria spp. Causing Gummosis of Peach Trees in Hubei Province, Central China
Authors: Wang Fan , Zhao Lina , Li Guohuai , Huang Junbin , Hsiang Tom
Published: April 2011

Peach (Prunus persica) is one of the most important and widely grown fruit trees in China; however, perennial gummosis on trunks and branches is a major problem in peach orchards of Hubei Province, one of the most important peach production areas of China. In order to identify the gummosis-causing agents, diseased trunks and branches were collected from 11 peach orchards in Hubei Province. Fungal isolates were obtained from these samples, yielding three species: Botryosphaeria dothidea (anamorph Fusicoccum aesculi), B. rhodina (anamorph Lasiodiplodia theobromae), and B. obtusa (anamorph Diplodia seriata). They were identified based on conidial morphology and cultural characteristics, as well as analyses of nucleotide sequences of three genomic regions: the internal transcribed spacer region, a partial sequence of the β-tubulin gene, and the translation elongation factor 1-α gene. Fusicoccum aesculi was found in all 11 orchards but L. theobromae was found only in Shayang County in the Jingmen region and D. seriata only in Gong'an County in the Jingzhou region. Via artificial inoculation using mycelia on wounded twigs or branches, these three species were all found to be pathogenic, causing dark lesions on the twigs and branches and, sometimes, gum exudation from diseased parts. Isolates of L. theobromae were the most virulent and caused the largest lesions and most copious gummosis, and D. seriata had less gum than the other two species. This report represents the first description of L. theobromae and D. seriata as causal agents of gummosis on peach in China.
Blood flow and coherent vortices in the normal and aneurysmatic aortas: a fluid dynamical approach to intra-luminal thrombus formation
Authors: Biasetti Jacopo , Hussain Fazle , Gasser T. Christian
Published: April 2011

Abdominal aortic aneurysms (AAAs) are frequently characterized by the development of an intra-luminal thrombus (ILT), which is known to have multiple biochemical and biomechanical implications. Development of the ILT is not well understood, and shear–stress-triggered activation of platelets could be the first step in its evolution. Vortical structures (VSs) in the flow affect platelet dynamics, which motivated the present study of a possible correlation between VS and ILT formation in AAAs. VSs educed by the
λ
2
-method using computational fluid dynamics simulations of the backward-facing step problem, normal aorta, fusiform AAA and saccular AAA were investigated. Patient-specific luminal geometries were reconstructed from computed tomography scans, and Newtonian and Carreau–Yasuda models were used to capture salient rheological features of blood flow. Particularly in complex flow domains, results depended on the constitutive model. VSs developed all along the normal aorta, showing that a clear correlation between VSs and high wall shear stress (WSS) existed, and that VSs started to break up during late systole. In contrast, in the fusiform AAA, large VSs developed at sites of tortuous geometry and high WSS, occupying the entire lumen, and lasting over the entire cardiac cycle. Downward motion of VSs in the AAA was in the range of a few centimetres per cardiac cycle, and with a VS burst at that location, the release (from VSs) of shear-stress-activated platelets and their deposition to the wall was within the lower part of the diseased artery, i.e. where the thickest ILT layer is typically observed. In the saccular AAA, only one VS was found near the healthy portion of the aorta, while in the aneurysmatic bulge, no VSs occurred. We present a fluid-dynamics-motivated mechanism for platelet activation, convection and deposition in AAAs that has the potential of improving our current understanding of the pathophysiology of fluid-driven ILT growth.
Migration by soaring or flapping: numerical atmospheric simulations reveal that turbulence kinetic energy dictates bee-eater flight mode
Authors: Sapir Nir , Horvitz Nir , Wikelski Martin , Avissar Roni , Mahrer Yitzhak , Nathan Ran
Published: April 2011

Aerial migrants commonly face atmospheric dynamics that may affect their movement and behaviour. Specifically, bird flight mode has been suggested to depend on convective updraught availability and tailwind assistance. However, this has not been tested thus far since both bird tracks and meteorological conditions are difficult to measure in detail throughout extended migratory flyways. Here, we applied, to our knowledge, the first comprehensive numerical atmospheric simulations by mean of the Regional Atmospheric Modeling System (RAMS) to study how meteorological processes affect the flight behaviour of migrating birds. We followed European bee-eaters (
Merops apiaster
) over southern Israel using radio telemetry and contrasted bird flight mode (flapping, soaring–gliding or mixed flight) against explanatory meteorological variables estimated by RAMS simulations at a spatial grid resolution of 250 × 250 m
2
. We found that temperature and especially turbulence kinetic energy (TKE) determine bee-eater flight mode, whereas, unexpectedly, no effect of tailwind assistance was found. TKE during soaring–gliding was significantly higher and distinct from TKE during flapping. We propose that applying detailed atmospheric simulations over extended migratory flyways can elucidate the highly dynamic behaviour of air-borne organisms, help predict the abundance and distribution of migrating birds, and aid in mitigating hazardous implications of bird migration.
Characterization of the effect of heat on agent strains of the transmissible spongiform encephalopathies
Authors: Somerville Robert A. , Gentles Nicola
Published: April 2011

The causal agents of the transmissible spongiform encephalopathy (TSE) diseases, sometimes called prion diseases, are characterized by high resistance to inactivation with heat. Results from thermal inactivation experiments on nine TSE strains, seven passaged in two PrP genotypes, showed differences in sensitivity to heat inactivation ranging over 17 °C. In addition, the rate of inactivation with increasing temperature varied between TSE models. In some cases passage in an alternative PrP genotype had little effect on the resulting inactivation properties, but for others the infectious agent was inactivated at lower temperatures. No strain with higher thermostability properties was selected. The effect of mixing two TSE strains, to see whether their properties were affected through interaction with each other, was also examined. The results showed that both strains behaved as expected from the behaviour of the unmixed controls, and that the strain responsible for inducing TSE disease could be identified. There was no evidence of a direct effect on intrinsic strain properties. Overall, the results illustrate the diversity in properties of TSE strains. They require intrinsic molecular properties of TSE agents to accommodate high resistance to inactivation and a mechanism, independent of the host, to directly encode these differences. These findings are more readily reconciled with models of TSE agents with two separate components, one of which is independent of the host and comprises a TSE-specific nucleic acid, than with models based solely on conformational changes to a host protein.
Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients
Authors: Köhler Anja , Gottschling Marc , Manning Kizzie , Lehmann Mandy D. , Schulz Eric , Krüger-Corcoran Daniela , Stockfleth Eggert , Nindl Ingo
Published: April 2011

Viral warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. The types of human papillomaviruses (HPV) in such lesions are different from that seen in the general population. A subset of these lesions is not infected with the classical wart-associated HPV types. In order to gain a better understanding of the HPV types in those lesions, we isolated ten novel HPVs from persisting keratotic lesions of immunosuppressed OTRs by rolling circle amplification and subsequent long-template PCR. Additionally, we sequenced and characterized the whole genome of the ten novel HPV types. Phylogenetic analyses revealed that nine HPV types belonged to the genus Gammapapillomavirus (γ-PV) and one to the genus Betapapillomavirus. In a phylogenetic analysis using L1 fragments of human and non-human PV types, primate papillomaviruses and our novel HPV types nested within the genus γ-PV in a highly polyphyletic pattern. This study significantly broadens the knowledge concerning the diversity and evolution of the poorly known γ-PV types.
Generation of neutralizing aptamers against herpes simplex virus type 2: potential components of multivalent microbicides
Authors: Moore M. D. , Bunka D. H. J. , Forzan M. , Spear P. G. , Stockley P. G. , McGowan I. , James W.
Published: April 2011

The prophylactic use of topical antiviral agents has recently been validated by the reduction in human immunodeficiency virus (HIV) type 1 infection incidence seen using tonofovir-containing microbicides. In order to develop a wide-spectrum microbicide to prevent infection with a wide range of sexually transmitted viruses, we have previously reported the development of HIV-neutralizing aptamers and here report the isolation and characterization of aptamers that neutralize herpes simplex virus type 2 (HSV-2). These aptamers bind the envelope glycoprotein (gD), are potent (IC50 of 20–50 nM) and are able to block infection pathways dependent on both major entry receptors, Nectin1 and HVEM. Structural analysis and mutagenesis of these aptamers reveal a core specificity element that could provide the basis for pharmaceutical development. As HSV-2 is a major risk factor for the acquisition of HIV-1, a microbicide capable of preventing HSV-2 infection would not only reduce the morbidity associated with HSV-2, but also that derived from HIV-1.
Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase
Authors: Lee Ji-Hye , Alam Intekhab , Han Kang Rok , Cho Sunyoung , Shin Sungho , Kang Seokha , Yang Jai Myung , Kim Kyung Hyun
Published: April 2011

Norovirus is one of the leading agents of gastroenteritis and is a major public health concern. In this study, the crystal structures of recombinant RNA-dependent RNA polymerase (RdRp) from murine norovirus-1 (MNV-1) and its complex with 5-fluorouracil (5FU) were determined at 2.5 Å resolution. Crystals with C2 symmetry revealed a dimer with half a dimer in the asymmetrical unit, and the protein exists predominantly as a monomer in solution, in equilibrium with a smaller population of dimers, trimers and hexamers. MNV-1 RdRp exhibited polymerization activity with a right-hand fold typical of polynucleotide polymerases. The metal ion modelled in close proximity to the active site was found to be coordinated tetrahedrally to the carboxyl groups of aspartate clusters. The orientation of 5FU observed in three molecules in the asymmetrical unit was found to be slightly different, but it was stabilized by a network of favourable interactions with the conserved active-site residues Arg185, Asp245, Asp346, Asp347 and Arg395. The information gained on the structural and functional features of MNV-1 RdRp will be helpful in understanding replication of norovirus and in designing novel therapeutic agents against this important pathogen.
Virally induced changes in cellular microRNAs maintain latency of human cytomegalovirus in CD34+ progenitors
Authors: Poole Emma , McGregor Dallas Stuart R. , Colston Julia , Joseph Robert Samuel V. , Sinclair John
Published: April 2011

One site of latency of human cytomegalovirus (HCMV; human herpesvirus 5) is known to be CD34+ haematopoietic progenitor cells, and it is likely that carriage of latent virus has profound effects on cellular gene expression in order to optimize latency and reactivation. As microRNAs (miRNAs) play important roles in regulating stem-cell gene expression, this study asked whether latent carriage of HCMV led to changes in cellular miRNA expression. A comprehensive miRNA screen showed the differential regulation of a number of cellular miRNAs during HCMV latency in CD34+ progenitor cells. One of these, hsa-miR-92a, was robustly decreased in three independent miRNA screens. Latency-induced change in hsa-miR-92a results in an increase in expression of GATA-2 and subsequent increased expression of cellular IL-10, which aids the maintenance of latent viral genomes in CD34+ cells, probably resulting from their increased survival.
Recombination in natural populations of watermelon mosaic virus: new agronomic threat or damp squib?
Authors: Desbiez C. , Joannon B. , Wipf-Scheibel C. , Chandeysson C. , Lecoq H.
Published: April 2011

Since their introduction in south-eastern France around 1999, new, ‘emerging’ (EM) strains of watermelon mosaic virus (WMV) coexist with the ‘classic’ (CL) strains present for more than 40 years. This situation constitutes a unique opportunity to estimate the frequency of recombinants appearing in the few years following introduction of new strains of a plant RNA virus. Molecular analyses performed on more than 1000 isolates from epidemiological surveys (2004–2008) and from experimental plots (2009–2010), and targeting only recombinants that became predominant in at least one plant, revealed at least seven independent CL/EM or EM/EM recombination events. The frequency of recombinants involving at least one EM parent in the natural populations tested was on the order of 1 %. No new recombinant was detected for more than 1 year, and none but one in more than one location. In tests comparing host range and aphid transmissibility, the new recombinants did not display a better fitness than their ‘parental’ isolates. No recombinant was detected from artificial mixed infections of CL and EM isolates of various hosts after testing more than 1500 subcultures obtained after single-aphid transmission. These results constitute one of the first estimations of the frequency of recombinants in natural conditions for a plant RNA virus. This suggests that although viable recombinants of WMV are not rare, and although recombination may potentially lead to new highly damaging strains, the new recombinants observed so far had a lower fitness than the parental strains and did not emerge durably in the populations.
Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase
Authors: Foeglein Ágnes , Loucaides Eva M. , Mura Manuela , Wise Helen M. , Barclay Wendy S. , Digard Paul
Published: April 2011

Avian influenza A viruses often do not propagate efficiently in mammalian cells. The viral polymerase protein PB2 is important for this host restriction, with amino-acid polymorphisms at residue 627 and other positions acting as ‘signatures’ of avian- or human-adapted viruses. Restriction is hypothesized to result from differential interactions (either positive or inhibitory) with unidentified cellular factors. We applied fluorescence recovery after photobleaching (FRAP) to investigate the mobility of the viral polymerase in the cell nucleus using A/PR/8/34 and A/Turkey/England/50-92/91 as model strains. As expected, transcriptional activity of a polymerase with the avian PB2 protein was strongly dependent on the identity of residue 627 in human but not avian cells, and this correlated with significantly slower diffusion of the inactive polymerase in human but not avian nuclei. In contrast, the activity and mobility of the PR8 polymerase was affected much less by residue 627. Sequence comparison followed by mutagenic analyses identified residues at known host-range-specific positions 271, 588 and 701 as well as a novel determinant at position 636 as contributors to host-specific activity of both PR8 and Turkey PB2 proteins. Furthermore, the correlation between poor transcriptional activity and slow diffusional mobility was maintained. However, activity did not obligatorily correlate with predicted surface charge of the 627 domain. Overall, our data support the hypothesis of a host nuclear factor that interacts with the viral polymerase and modulates its activity. While we cannot distinguish between positive and inhibitory effects, the data have implications for how such factors might operate.
ABI3 and PIL5 Collaboratively Activate the Expression ofSOMNUSby Directly Binding to Its Promoter in ImbibedArabidopsisSeeds
Authors: Park Jeongmoo , Lee Nayoung , Kim Woohyun , Lim Soohwan , Choi Giltsu
Published: April 2011

A previous study showed that SOMNUS (SOM), which encodes a C3H-type zinc finger protein, is a key negative regulator of seed germination that acts downstream of PHYTOCHROME INTERACTING FACTOR3-LIKE5 (PIL5). However, it was not determined if PIL5 is the sole regulator of SOM expression. Public microarray data suggest that the expression of SOM mRNA is regulated also by ABSCISIC ACID INSENSITIVE3 (ABI3), another key regulator of seed germination. By analyzing abi3 mutants and ABI3 overexpression lines, we show here that ABI3 activates the expression of SOM mRNA collaboratively with PIL5 in imbibed seeds. Chromatin immunoprecipitation analysis coupled with electrophoretic mobility shift assay indicate that ABI3 activates the expression of SOM mRNA by directly binding to two RY motifs present in the SOM promoter in vivo, which is further supported by the greatly decreased expression of a reporter gene driven by a SOM promoter bearing mutated RY motifs. At the protein level, the ABI3 protein interacts with the PIL5 protein. The ABI3-PIL5 interaction, however, does not affect targeting of ABI3 and PIL5 to SOM promoters. Taken together, our results indicate that ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter.
MATE2 Mediates Vacuolar Sequestration of Flavonoid Glycosides and Glycoside Malonates inMedicago truncatula
Authors: Zhao Jian , Huhman David , Shadle Gail , He Xian-Zhi , Sumner Lloyd W. , Tang Yuhong , Dixon Richard A.
Published: April 2011

The majority of flavonoids, such as anthocyanins, proanthocyanidins, and isoflavones, are stored in the central vacuole, but the molecular basis of flavonoid transport is still poorly understood. Here, we report the functional characterization of a multidrug and toxin extrusion transporter (MATE2), from Medicago truncatula. MATE 2 is expressed primarily in leaves and flowers. Despite its high similarity to the epicatechin 3′-O-glucoside transporter MATE1, MATE2 cannot efficiently transport proanthocyanidin precursors. In contrast, MATE2 shows higher transport capacity for anthocyanins and lower efficiency for other flavonoid glycosides. Three malonyltransferases that are coexpressed with MATE2 were identified. The malonylated flavonoid glucosides generated by these malonyltransferases are more efficiently taken up into MATE2-containing membrane vesicles than are the parent glycosides. Malonylation increases both the affinity and transport efficiency of flavonoid glucosides for uptake by MATE2. Genetic loss of MATE2 function leads to the disappearance of leaf anthocyanin pigmentation and pale flower color as a result of drastic decreases in the levels of various flavonoids. However, some flavonoid glycoside malonates accumulate to higher levels in MATE2 knockouts than in wild-type controls. Deletion of MATE2 increases seed proanthocyanidin biosynthesis, presumably via redirection of metabolic flux from anthocyanin storage.
Unlocking the Barley Genome by Chromosomal and Comparative Genomics
Authors: Mayer Klaus F.X. , Martis Mihaela , Hedley Pete E. , Šimková Hana , Liu Hui , Morris Jenny A. , Steuernagel Burkhard , Taudien Stefan , Roessner Stephan , Gundlach Heidrun , Kubaláková Marie , Suchánková Pavla , Murat Florent , Felder Marius , Nussbaumer Thomas , Graner Andreas , Salse Jerome , Endo Takashi , Sakai Hiroaki , Tanaka Tsuyoshi , Itoh Takeshi , Sato Kazuhiro , Platzer Matthias , Matsumoto Takashi , Scholz Uwe , Doležel Jaroslav , Waugh Robbie , Stein Nils
Published: April 2011

We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
A Sister Group Contrast Using Untargeted Global Metabolomic Analysis Delineates the Biochemical Regulation Underlying Desiccation Tolerance in Sporobolus stapfianus
Authors: Oliver Melvin J. , Guo Lining , Alexander Danny C. , Ryals John A. , Wone Bernard W.M. , Cushman John C.
Published: April 2011

Understanding how plants tolerate dehydration is a prerequisite for developing novel strategies for improving drought tolerance. The desiccation-tolerant (DT) Sporobolus stapfianus and the desiccation-sensitive (DS) Sporobolus pyramidalis formed a sister group contrast to reveal adaptive metabolic responses to dehydration using untargeted global metabolomic analysis. Young leaves from both grasses at full hydration or at 60% relative water content (RWC) and from S. stapfianus at lower RWCs were analyzed using liquid and gas chromatography linked to mass spectrometry or tandem mass spectrometry. Comparison of the two species in the fully hydrated state revealed intrinsic differences between the two metabolomes. S. stapfianus had higher concentrations of osmolytes, lower concentrations of metabolites associated with energy metabolism, and higher concentrations of nitrogen metabolites, suggesting that it is primed metabolically for dehydration stress. Further reduction of the leaf RWC to 60% instigated a metabolic shift in S. stapfianus toward the production of protective compounds, whereas S. pyramidalis responded differently. The metabolomes of S. stapfianus leaves below 40% RWC were strongly directed toward antioxidant production, nitrogen remobilization, ammonia detoxification, and soluble sugar production. Collectively, the metabolic profiles obtained uncovered a cascade of biochemical regulation strategies critical to the survival of S. stapfianus under desiccation.
Quantification of the maternal–embryonal nutritional relationship of elasmobranchs: case study of wobbegong sharks (genus Orectolobus)
Authors: Huveneers C. , Otway N. M. , Harcourt R. G. , Ellis M.
Published: April 2011

The present study used wobbegong sharks (genus Orectolobus) to assess the threshold value proposed by previous research to categorize strict lecithotrophic from incipient histotrophic species. Totals of 236 and 135 ornate wobbegong Orectolobus ornatus and spotted wobbegong Orectolobus maculatus, respectively, were collected from the New South Wales commercial fishery between June 2003 and May 2006. Eight pregnant gulf wobbegong Orectolobus halei were also recorded outside the sampling period for the first time. The three species were reproductively synchronous with a gestation of c. 10–11 months. Embryos started to be macroscopically visible during January and external yolk sacs were fully absorbed by June to July when embryos were c. 200 mm total length (LT). Internal yolk sacs were first observed during April to May when embryos were c. 160 mm LT, reached a peak during June and persisted in embryos immediately prior to parturition. The total wet mass from uterine egg to full‐term embryos increased by 44–89% and 45–62%, whereas the total organic mass decreased by 32–33% and 26%, for O. ornatus and O. maculatus, respectively, suggesting that these species are strict lecithotrophic yolk‐sac viviparous sharks with no maternal nutrient input. A review of the literature identified various issues and suggested that the previously proposed organic mass loss threshold value separating strict lecithotrophic species from incipient histotrophic species might not be appropriate. Instead, it is recommended that a combination of methods (e.g. estimation of organic mass gain or loss between ovarian egg and developed embryo, histology and electron microscopy of the uterus, radio‐tracer assay and uterine fluid analysis throughout gestation) is used to discern between strict lecithotrophic and incipient histotrophic species.
Post‐release feeding and growth of hatchery‐reared Japanese flounder Paralichthys olivaceus: relevance to stocking effectiveness
Authors: Tomiyama T. , Watanabe M. , Kawata G. , Ebe K.
Published: April 2011

The feeding and growth of hatchery‐reared (HR) Japanese flounder Paralichthys olivaceus of c. 100 mm total length (LT) released off the coast of Fukushima, Japan, were investigated. From 2 to 15 days after release, the HR P. olivaceus frequently exhibited high empty‐stomach frequency (>40%), low stomach‐content mass (<1% of body mass), reduced somatic condition from release (c.−10%) and negligible growth. Thereafter, empty‐stomach frequency decreased, the stomach‐content mass of HR fish increased to 2–8% of body mass, the somatic condition recovered and growth rate increased to 0·5–1·5 mm day−1. Prey items were initially mysids, shifting thereafter to fishes such as the Japanese anchovy Engraulis japonica, as observed similarly in wild counterparts. The proportion of mysids decreased with time after release irrespective of size at release, indicating the importance of mysids for adaptation to natural food. Recapture rates at age 1 year, derived from fish market surveys, varied greatly among release years (4–11%). The variation in the recapture rates was largely accounted for by the post‐release growth rates (r2 = 0·5), suggesting a relationship between the post‐release growth of HR fish and their survival and subsequent stocking effectiveness.
Musculoskeletal structure of the feeding system and implications of snout elongation in Hippocampus reidi and Dunckerocampus dactyliophorus
Authors: Leysen H. , Christiaens J. , De Kegel B. , Boone M. N. , Van Hoorebeke L. , Adriaens D.
Published: April 2011

A thorough morphological description of the feeding apparatus in Hippocampus reidi, a long‐snouted seahorse, and Dunckerocampus dactyliophorus, an extremely long‐snouted pipefish, revealed specialized features that might be associated with the fast and powerful suction feeding, like the two ligamentous connections between the lower jaw and the hyoid, the saddle joint of the latter with the suspensorium and the vertebro‐pectoral fusion that articulates on three points with the cranium. Despite the conserved morphology of the feeding apparatus, it was found that in H. reidi the orientation of the occipital joint is ventrocaudal, the sternohyoideus and epaxial muscles are more bulky and both have a short tendon. In D. dactyliophorus, on the other hand, the protractor hyoidei muscle is enclosed by the mandibulo‐hyoid ligament, the sternohyoideus and epaxial tendons are long and a sesamoid bone is present in the latter. These features were compared to other syngnathid species with different snout lengths to evaluate the implications of snout elongation on the musculoskeletal structure of the cranium. The arched path of the adductor mandibulae and the greater rigidity of the lower jaw might be related to elongation of the snout, as it yields an increased mechanical advantage of the lower jaw system and a reduced torque between the elements of the lower jaw during protractor hyoidei muscle contraction, respectively. Nevertheless, most observed features did not seem to be related to snout length, but might be associated with different force‐generating strategies.