bluuebunny/crossref_metadata_2025 huggingface dataset:
Organic photodiodes on the base of cotton fibers/polymer composite
Authors: Zakirov A. S. , Yuldashev Sh. U. , Cho H. D. , Lee J. C. , Kang T. W. , Mamadalimov A. T.
Published: December 2011

In this paper, we report a study on the optical and electrical properties of pure cotton fibers from chemically surface and morphology modified and coated with poly [2-methoxy-5-(2-ethylhexyloxy)-1, 4-phenylenevinylene] (MEH-PPV) polymer samples by the dip-coating method. The treated and coated fibers properties were characterized by using scanning electron microscopy (SEM), photoluminescence, and I–V characteristics. The performance of fibers with the MEH-PPV polymer as a coating component was investigated and an excellent white-light emission which consists of blue-, green-, and red-light-emitting bands was demonstrated. I–V characteristics of the sandwich-type devices consisting of successive layers of ITO–PEDOT-PSS- CF/MEH-PPV–Ag show that upon light illumination the current increases in both the forward and reverse bias conditions which suggest that the photoresponse parameters for the heterojunction are better than the composite alone.
Enhancement of linear and nonlinear optical properties of deoxyribonucleic acid-silica thin films doped with rhodamine
Authors: Sahraoui Bouchta , Pranaitis Mindaugas , Iliopoulos Konstantinos , Mihaly Maria , Comanescu Alina F. , Moldoveanu Mirela , Rau Ileana , Kažukauskas Vaidotas
Published: December 2011

In this work, we present the linear and nonlinear optical properties of DNA as functional material, incorporated into a silica material matrix with rhodamine organic dye. We observed that even low concentration of DNA affects the aggregate behavior of the dyes in silica films. The samples with DNA showed higher transmittance and fluorescence efficiency. Moreover, the presence of DNA has been found to significantly enhance the nonlinear optical response of the systems. In this way, we prove that silica materials can provide suitable matrices for hybridization with functional molecules and can be utilized as active optical waveguide materials with enhanced nonlinear optical properties.
Tuning the austenite and martensite phase fraction in ferromagnetic shape memory alloy ribbons of Ni45Co5Mn38Sn12
Authors: Lakhani Archana , Dash S. , Banerjee A. , Chaddah P. , Chen X. , Ramanujan R. V.
Published: December 2011

The ferromagnetic shape memory alloy ribbons with composition Ni45Co5Mn38Sn12 are shown to have field induced kinetically arrested ferromagnetic austenite phase down to the low temperature due to hindered martensite transformation. This gives rise to the coexisting martensite and austenite phases in a wide range of temperature and field. Here, we show a systematic rise in arrested austenite phase with the reduction in martensite phase quantitatively by various magnetization measurements. The fraction of these coexisting phases can be tuned in “field-temperature” space. Further, we show that the “domain” of tunability varies with temperature.
High-quality {20-21} GaN layers on patterned sapphire substrate with wide-terrace
Authors: Okada Narihito , Oshita Hiroyasu , Yamane Keisuke , Tadatomo Kazuyuki
Published: December 2011

A {20-21} GaN layer was grown from a c-plane-like sapphire sidewall of a {22-43} patterned sapphire substrate according to the epitaxial relationship between c-GaN and c-sapphire despite {20-21} GaN is not growing on {22-43} sapphire. The as-grown {20-21} GaN layer had an m- and {10-11} facet structure. To improve the {20-21} GaN layer, a wide-terrace was attempted. The defects in the GaN layer were clustered on the m-facets, resulting in a dislocation density of less than 5.6 × 105/cm2 on the {10-11} facets. The {20-21} GaN layer had an excellent photoluminescence spectrum indicating a small number of defects.
Total routing and absorption of photons in dual color plasmonic antennas
Authors: Koechlin Charlie , Bouchon Patrick , Pardo Fabrice , Jaeck Julien , Lafosse Xavier , Pelouard Jean-Luc , Haïdar Riad
Published: December 2011

We present both theoretical and experimental evidence that two metal-insulator-metal plasmonic resonators can be combined into a wideband and total photon absorber in the mid-infrared. We show that, although closely arranged in a subwavelength period, these resonators behave as angularly independent antennas at their own resonant wavelength. The structures thus allow for an efficient dual color photon routing and collection.
Theoretical study on phase locking of the array of fiber lasers coupled by bi-dimensional mutual injection
Authors: Cao Jianqiu , Lu Qisheng , Hou Jing , Xu Xiaojun , Guo Shaofeng
Published: December 2011

In this paper, the array of fiber lasers coupled by bi-dimensional mutual injection is firstly, to our knowledge, investigated. Phase locking of the array is theoretically studied and the phase-locked states of the array are given. It is found that the array with bi-dimensional mutual injection can export the same amount of the phase-locked states as the array with one-dimensional mutual injection, which implies that the amount of phase-locked states does not depend on the dimension of mutual injection. The conditions needed for phase locking of the array are also studied. It is illuminated that, compared with the array with one-dimensional mutual injection, more conditions are needed for phase locking of the array with bi-dimensional mutual injection. Based on these results, the options for improving the performance of the array of fiber lasers coupled by mutual injection are discussed.
Soil phosphorus supply affects nodulation and N:P ratio in 11 perennial legume seedlings
Authors: Pang Jiayin , Tibbett Mark , Denton Matthew D. , Lambers Hans , Siddique Kadambot H. M. , Ryan Megan H.
Published: December 2011

Developing new perennial pasture legumes for low-P soils is a priority for Australian Mediterranean agro-ecosystems, where soil P availability is naturally low. As legumes tend to require higher P inputs than non-legumes, the ability of these plants to fix N2 under varying soil P levels must be determined. Therefore, the objective of this study was to investigate the influence of soil P supply on plant N status and nodule formation in 11 perennial legumes, including some novel pasture species. We investigated the effect of applying soil P, ranging from 0 to 384 μg P/g dry soil, on plant N status and nodulation in a glasshouse. Without exogenous P supply, shoot N concentration and N : P ratio were higher than at 6 μg P/g soil. Shoot N concentration and N : P ratio then changed little with further increase in P supply. There was a close positive correlation between the number of nodules and shoot P concentration in 7 of the 11 species. Total nodule dry weight and the percentage of plant dry weight that consisted of nodules increased when P supply increased from 6 to 48 μg P/g. Without exogenous P addition, N : P ratios partitioned into a two-group distribution, with species having a N : P ratio of either >70 or <50 g/g. We suggest that plants with a high N : P ratio may take up N from the soil constitutively, while those with a low N : P ratio may regulate their N uptake in relation to internal P concentration. The flexibility of the novel pasture legumes in this study to adjust their leaf N concentrations under different levels of soil P supplements other published evidence of good growth and high P uptake and P-use efficiency under low soil P supply and suggests their potential as pasture plants in low-P soils in Australian Mediterranean agro-ecosystems warrants further attention.
Interaction between plant genotype and the symbiosis with Epichloë fungal endophytes in seeds of red fescue (Festuca rubra)
Authors: Gundel P. E. , Zabalgogeazcoa I. , Vázquez de Aldana B. R.
Published: December 2011

In diverse natural habitats of Europe, plants of Festuca rubra are commonly infected by the fungal endophyte Epichloë festucae. Under several circumstances, the association between the grass and the fungus has been shown to be mutualistic. Here, we conducted an experiment to study the differences in seed germination and mortality between infected (E+) and endophyte-free plants (E–) at different temperatures (12 and 25°C) and water potentials (0 and –0.5 MPa). Three half-sib lines of F. rubra, each composed of E+ and E– seeds, and derived from infected plants from semiarid grasslands were used. Although the endophyte effect depended on the incubation condition, germination percentage was significantly greater for E– (52%) than for E+ seeds (41%). Seed germination was more inhibited by the low water potential (75 v. 24% for –0.5 and 0.0 MPa, respectively), than by the high temperature (64 v. 35% for 25 and 12°C, respectively). However, mortality was highly dependent on the interaction between plant genotype and endophyte, and between temperature and water condition. It is remarkable that while highly dependent on the host genotype, there was a clear effect of endophyte increasing seed survival, especially in those treatments that were unfavourable for germination. For example, in the more restrictive treatment (25°C and –0.5 MPa), seed survival was on average, 44 and 39% for E+ and E–, respectively. In general, the endophyte affected seed characteristics of F. rubra by reducing the percentage of germination, but simultaneously increasing seed survival.
Carbon and sulfur back flux during anaerobic microbial oxidation of methane and coupled sulfate reduction
Authors: Holler Thomas , Wegener Gunter , Niemann Helge , Deusner Christian , Ferdelman Timothy G. , Boetius Antje , Brunner Benjamin , Widdel Friedrich
Published: December 2011

Microbial degradation of substrates to terminal products is commonly understood as a unidirectional process. In individual enzymatic reactions, however, reversibility (reverse reaction and product back flux) is common. Hence, it is possible that entire pathways of microbial degradation are associated with back flux from the accumulating product pool through intracellular intermediates into the substrate pool. We investigated carbon and sulfur back flux during the anaerobic oxidation of methane (AOM) with sulfate, one of the least exergonic microbial catabolic processes known. The involved enzymes must operate not far from the thermodynamic equilibrium. Such an energetic situation is likely to favor product back flux. Indeed, cultures of highly enriched archaeal–bacterial consortia, performing net AOM with unlabeled methane and sulfate, converted label from14C-bicarbonate and35S-sulfide to14C-methane and35S-sulfate, respectively. Back fluxes reached 5% and 13%, respectively, of the net AOM rate. The existence of catabolic back fluxes in the reverse direction of net reactions has implications for biogeochemical isotope studies. In environments where biochemical processes are close to thermodynamic equilibrium, measured fluxes of labeled substrates to products are not equal to microbial net rates. Detection of a reaction in situ by labeling may not even indicate a net reaction occurring in the direction of label conversion but may reflect the reverse component of a so far unrecognized net reaction. Furthermore, the natural isotopic composition of the substrate and product pool will be determined by both the forward and back flux. This finding may have to be considered in the interpretation of stable isotope records.
Drosophila
Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line
Authors: Wang Sidney H. , Elgin Sarah C. R.
Published: December 2011

Transposon control is a critical process during reproduction. The PIWI family proteins can play a key role, using a piRNA-mediated slicing mechanism to suppress transposon activity posttranscriptionally. In
Drosophila melanogaster
, Piwi is predominantly localized in the nucleus and has been implicated in heterochromatin formation. Here, we use female germ-line–specific depletion to study Piwi function. This depletion of Piwi leads to infertility and to axis specification defects in the developing egg chambers; correspondingly, widespread loss of transposon silencing is observed. Germ-line Piwi does not appear to be required for piRNA production. Instead, Piwi requires Aubergine (and presumably secondary piRNA) for proper localization. A subset of transposons that show significant overexpression in germ-line Piwi-depleted ovaries exhibit a corresponding loss of HP1a and H3K9me2. Germ-line HP1a depletion also leads to a loss of transposon silencing, demonstrating the functional requirement for HP1a enrichment at these loci. Considering our results and those of others, we infer that germ-line Piwi functions downstream of piRNA production to promote silencing of some transposons via recruitment of HP1a. Thus, in addition to its better-known function in posttranscriptional silencing, piRNA also appears to function in a targeting mechanism for heterochromatin formation mediated by Piwi.
Experience-dependent regulation of CaMKII activity within single visual cortex synapses in vivo
Authors: Mower Amanda F. , Kwok Showming , Yu Hongbo , Majewska Ania K. , Okamoto Ken-Ichi , Hayashi Yasunori , Sur Mriganka
Published: December 2011

Unbalanced visual input during development induces persistent alterations in the function and structure of visual cortical neurons. The molecular mechanisms that drive activity-dependent changes await direct visualization of underlying signals at individual synapses in vivo. By using a genetically engineered Förster resonance energy transfer (FRET) probe for the detection of CaMKII activity, and two-photon imaging of single synapses within identified functional domains, we have revealed unexpected and differential mechanisms in specific subsets of synapses in vivo. Brief monocular deprivation leads to activation of CaMKII in most synapses of layer 2/3 pyramidal cells within deprived eye domains, despite reduced visual drive, but not in nondeprived eye domains. Synapses that are eliminated in deprived eye domains have low basal CaMKII activity, implying a protective role for activated CaMKII against synapse elimination.
A macrocyclic HCV NS3/4A protease inhibitor interacts with protease and helicase residues in the complex with its full-length target
Authors: Schiering Nikolaus , D’Arcy Allan , Villard Frederic , Simić Oliver , Kamke Marion , Monnet Gaby , Hassiepen Ulrich , Svergun Dmitri I. , Pulfer Ruth , Eder Jörg , Raman Prakash , Bodendorf Ursula
Published: December 2011

Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV NS3 protein is essential for viral polyprotein processing and RNA replication and hence viral replication. It is composed of an N-terminal serine protease domain and a C-terminal helicase/NTPase domain. For full activity, the protease requires the NS4A protein as a cofactor. HCV NS3/4A protease is a prime target for developing direct-acting antiviral agents. First-generation NS3/4A protease inhibitors have recently been introduced into clinical practice, markedly changing HCV treatment options. To date, crystal structures of HCV NS3/4A protease inhibitors have only been reported in complex with the protease domain alone. Here, we present a unique structure of an inhibitor bound to the full-length, bifunctional protease-helicase NS3/4A and show that parts of the P4 capping and P2 moieties of the inhibitor interact with both protease and helicase residues. The structure sheds light on inhibitor binding to the more physiologically relevant form of the enzyme and supports exploring inhibitor-helicase interactions in the design of the next generation of HCV NS3/4A protease inhibitors. In addition, small angle X-ray scattering confirmed the observed protease-helicase domain assembly in solution.
Antagonistic gene transcripts regulate adaptation to new growth environments
Authors: Baumgartner Bridget L. , Bennett Matthew R. , Ferry Michael , Johnson Tracy L. , Tsimring Lev S. , Hasty Jeff
Published: December 2011

Cells have evolved complex regulatory networks that reorganize gene expression patterns in response to changing environmental conditions. These changes often involve redundant mechanisms that affect various levels of gene expression. Here, we examine the consequences of enhanced mRNA degradation in the galactose utilization network of
Saccharomyces cerevisiae
. We observe that glucose-induced degradation of GAL1 transcripts provides a transient growth advantage to cells upon addition of glucose. We show that the advantage arises from relief of translational competition between GAL1 transcripts and those of cyclin CLN3, a translationally regulated initiator of cell division. This competition creates a translational bottleneck that balances the production of Gal1p and Cln3p and represents a posttranscriptional control mechanism that enhances the cell's ability to adapt to changes in carbon source. We present evidence that the spatial regulation of GAL1 and CLN3 transcripts is what allows growth to be maintained during fluctuations of glucose availability. Our results provide unique insights into how cells optimize energy use during growth in a dynamic environment.
Neuronal differentiation by TAp73 is mediated by microRNA-34a regulation of synaptic protein targets
Authors: Agostini Massimiliano , Tucci Paola , Killick Richard , Candi Eleonora , Sayan Berna S. , Rivetti di val Cervo Pia , Nicotera Pierluigi , McKeon Frank , Knight Richard A. , Mak Tak W. , Melino Gerry
Published: December 2011

The p53-family member TAp73 is a transcription factor that plays a key role in many biological processes. Here, we show that p73 drives the expression of microRNA (miR)-34a, but not miR-34b and -c, by acting on specific binding sites on the miR-34a promoter. Expression of miR-34a is modulated in parallel with that of TAp73 during in vitro differentiation of neuroblastoma cells and cortical neurons. Retinoid-driven neuroblastoma differentiation is inhibited by knockdown of either p73 or miR-34a. Transcript expression of miR-34a is significantly reduced in vivo both in the cortex and hippocampus of p73
−/−
mice; miR-34a and TAp73 expression also increase during postnatal development of the brain and cerebellum when synaptogenesis occurs. Accordingly, overexpression or silencing of miR-34a inversely modulates expression of synaptic targets, including synaptotagmin-1 and syntaxin-1A. Notably, the axis TAp73/miR-34a/synaptotagmin-1 is conserved in brains from Alzheimer's patients. These data reinforce a role for TAp73 in neuronal development.
Dysregulation of Kruppel-like factor 4 during brain development leads to hydrocephalus in mice
Authors: Qin Song , Liu Menglu , Niu Wenze , Zhang Chun-Li
Published: December 2011

Kruppel-like factor 4 (KLF4) is involved in self-renewal of embryonic stem cells and reprogramming of somatic cells to pluripotency. However, its role in lineage-committed stem cells remains largely unknown. Here, we show that KLF4 is expressed in neural stem cells (NSCs) and is down-regulated during neuronal differentiation. Unexpectedly, enhanced expression of KLF4 reduces self-renewal of cultured NSCs and inhibits proliferation of subventricular neural precursors in transgenic mice. Mice with increased KLF4 in NSCs and NSCs-derived ependymal cells developed hydrocephalus-like characteristics, including enlarged ventricles, thinned cortex, agenesis of the corpus callosum, and significantly reduced subcommissural organ. These characteristics were accompanied by elevation of GFAP expression and astrocyte hypertrophy. The ventricular cilia, vital for cerebrospinal fluid flow, are also disrupted in the mutant mice. These results indicate that down-regulation of KLF4 is critical for neural development and its dysregulation may lead to hydrocephalus.
Structural interconversions modulate activity of
Escherichia coli
ribonucleotide reductase
Authors: Ando Nozomi , Brignole Edward J. , Zimanyi Christina M. , Funk Michael A. , Yokoyama Kenichi , Asturias Francisco J. , Stubbe JoAnne , Drennan Catherine L.
Published: December 2011

Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the catalytic subunit (
α
2
) and the radical-generation subunit (
β
2
) interact. Here we present the first structure of a complex between
α
2
and
β
2
subunits for the prototypic RNR from
Escherichia coli
. Using four techniques (small-angle X-ray scattering, X-ray crystallography, electron microscopy, and analytical ultracentrifugation), we describe an unprecedented
α
4
β
4
ring-like structure in the presence of the negative activity effector dATP and provide structural support for an active
α
2
β
2
configuration. We demonstrate that, under physiological conditions,
E. coli
RNR exists as a mixture of transient
α
2
β
2
and
α
4
β
4
species whose distributions are modulated by allosteric effectors. We further show that this interconversion between
α
2
β
2
and
α
4
β
4
entails dramatic subunit rearrangements, providing a stunning molecular explanation for the allosteric regulation of RNR activity in
E. coli
.
Specific neural substrate linking respiration to locomotion
Authors: Gariépy Jean-François , Missaghi Kianoush , Chevallier Stéphanie , Chartré Shannon , Robert Maxime , Auclair François , Lund James P. , Dubuc Réjean
Published: December 2011

When animals move, respiration increases to adapt for increased energy demands; the underlying mechanisms are still not understood. We investigated the neural substrates underlying the respiratory changes in relation to movement in lampreys. We showed that respiration increases following stimulation of the mesencephalic locomotor region (MLR) in an in vitro isolated preparation, an effect that persists in the absence of the spinal cord and caudal brainstem. By using electrophysiological and anatomical techniques, including whole-cell patch recordings, we identified a subset of neurons located in the dorsal MLR that send direct inputs to neurons in the respiratory generator. In semi-intact preparations, blockade of this region with 6-cyano-7-nitroquinoxaline-2,3-dione and (2R)-amino-5-phosphonovaleric acid greatly reduced the respiratory increases without affecting the locomotor movements. These results show that neurons in the respiratory generator receive direct glutamatergic connections from the MLR and that a subpopulation of MLR neurons plays a key role in the respiratory changes linked to movement.
Variable motif utilization in homeotic selector (Hox)–cofactor complex formation controls specificity
Authors: Lelli Katherine M. , Noro Barbara , Mann Richard S.
Published: December 2011

Homeotic selector (Hox) proteins often bind DNA cooperatively with cofactors such as Extradenticle (Exd) and Homothorax (Hth) to achieve functional specificity in vivo. Previous studies identified the Hox YPWM motif as an important Exd interaction motif. Using a comparative approach, we characterize the contribution of this and additional conserved sequence motifs to the regulation of specific target genes for three
Drosophila
Hox proteins. We find that Sex combs reduced (Scr) uses a simple interaction mechanism, where a single tryptophan-containing motif is necessary for Exd-dependent DNA-binding and in vivo functions. Abdominal-A (AbdA) is more complex, using multiple conserved motifs in a context-dependent manner. Lastly, Ultrabithorax (Ubx) is the most flexible, in that it uses multiple conserved motifs that function in parallel to regulate target genes in vivo. We propose that using different binding mechanisms with the same cofactor may be one strategy to achieve functional specificity in vivo.
Solar hydrogen-producing bionanodevice outperforms natural photosynthesis
Authors: Lubner Carolyn E. , Applegate Amanda M. , Knörzer Philipp , Ganago Alexander , Bryant Donald A. , Happe Thomas , Golbeck John H.
Published: December 2011

Although a number of solar biohydrogen systems employing photosystem I (PSI) have been developed, few attain the electron transfer throughput of oxygenic photosynthesis. We have optimized a biological/organic nanoconstruct that directly tethers F
B
, the terminal [4Fe-4S] cluster of PSI from
Synechococcus
sp. PCC 7002, to the distal [4Fe-4S] cluster of the [FeFe]-hydrogenase (H
2
ase) from
Clostridium acetobutylicum
. On illumination, the PSI–[FeFe]-H
2
ase nanoconstruct evolves H
2
at a rate of 2,200 ± 460 
μ
mol mg chlorophyll
-1
 h
-1
, which is equivalent to 105 ± 22 e
-
PSI
-1
 s
-1
. Cyanobacteria evolve O
2
at a rate of approximately 400 
μ
mol mg chlorophyll
-1
 h
-1
, which is equivalent to 47 e
-
PSI
-1
 s
-1
, given a PSI to photosystem II ratio of 1.8. The greater than twofold electron throughput by this hybrid biological/organic nanoconstruct over in vivo oxygenic photosynthesis validates the concept of tethering proteins through their redox cofactors to overcome diffusion-based rate limitations on electron transfer.
Proton-coupled electron transfer at modified electrodes by multiple pathways
Authors: Chen Zuofeng , Vannucci Aaron K. , Concepcion Javier J. , Jurss Jonah W. , Meyer Thomas J.
Published: December 2011

In single site water or hydrocarbon oxidation catalysis with polypyridyl Ru complexes such as [Ru
II
(Mebimpy)(bpy)(H
2
O)]
2+
[where bpy is 2,2′-bipyridine, and Mebimpy is 2,6-bis(1-methylbenzimidazol-2-yl)pyridine]
2
, or its surface-bound analog [Ru
II
(Mebimpy)(4,4
′
-bis-methlylenephosphonato-2,2
′
-bipyridine)(OH
2
)]
2+
2
-
PO

3

H

2

, accessing the reactive states, Ru
V
 = O
3+
/Ru
IV
 = O
2+
, at the electrode interface is typically rate limiting. The higher oxidation states are accessible by proton-coupled electron transfer oxidation of aqua precursors, but access at inert electrodes is kinetically inhibited. The inhibition arises from stepwise mechanisms which impose high energy barriers for 1e
-
intermediates. Oxidation of the Ru
III
-OH
2+
or

forms of
2
-
PO

3

H

2

to Ru
IV
 = O
2+
on planar fluoride-doped SnO
2
electrode and in nanostructured films of Sn(IV)-doped In
2
O
3
and TiO
2
has been investigated with a focus on identifying microscopic phenomena. The results provide direct evidence for important roles for the nature of the electrode, temperature, surface coverage, added buffer base, pH, solvent, and solvent H
2
O/D
2
O isotope effects. In the nonaqueous solvent, propylene carbonate, there is evidence for a role for surface-bound phosphonate groups as proton acceptors.
Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes
Authors: King Heather M. , Shubin Neil H. , Coates Michael I. , Hale Melina E.
Published: December 2011

Tetrapods evolved from sarcopterygian fishes in the Devonian and were the first vertebrates to colonize land. The locomotor component of this transition can be divided into four major events: terrestriality, the origins of digited limbs, solid substrate-based locomotion, and alternating gaits that use pelvic appendages as major propulsors. As the sister group to tetrapods, lungfish are a morphologically and phylogenetically relevant sarcopterygian taxon for understanding the order in which these events occurred. We found that a species of African lungfish (Protopterus annectens) uses a range of pelvic fin-driven, tetrapod-like gaits, including walking and bounding, in an aquatic environment, despite having a derived limb endoskeleton and primitively small, muscularly supported pelvis. Surprisingly, given these morphological traits,P. annectensalso lifts its body clear of the substrate using its pelvic fins, an ability thought to be a tetrapod innovation. Our findings suggest that some fundamental features of tetrapod locomotion, including pelvic limb gait patterns and substrate association, probably arose in sarcopterygians before the origin of digited limbs or terrestriality. It follows that the attribution of some of the nondigited Devonian fossil trackways to limbed tetrapods may need to be revisited.
Reasoning about knowledge using defeasible logic
Authors: Walton Douglas
Published: December 2011

In this paper, the Carneades argumentation system is extended to represent a procedural view of inquiry in which evidence is marshalled to support or defeat claims to knowledge. The model is a sequence of moves in a collaborative group inquiry in which parties take turns making assertions about what is known or not known, putting forward evidence to support them, and subjecting these moves to criticisms. It is shown how this model of evaluating evidence in an inquiry is based on a defeasible logic using forms of argument that admit exceptions. It is contended that reasoning from absence of knowledge is as important to inquiry as positive reasoning from evidence to knowledge. The philosophical conflict between this view of reasoning about knowledge and the true-belief-plus view is explored by airing objections and replies on both sides.
Memory B cells, but not long-lived plasma cells, possess antigen specificities for viral escape mutants
Authors: Purtha Whitney E. , Tedder Thomas F. , Johnson Syd , Bhattacharya Deepta , Diamond Michael S.
Published: December 2011

Memory B cells (MBCs) and long-lived plasma cells (LLPCs) persist after clearance of infection, yet the specific and nonredundant role MBCs play in subsequent protection is unclear. After resolution of West Nile virus infection in mice, we demonstrate that LLPCs were specific for a single dominant neutralizing epitope, such that immune serum poorly inhibited a variant virus that encoded a mutation at this critical epitope. In contrast, a large fraction of MBC produced antibody that recognized both wild-type (WT) and mutant viral epitopes. Accordingly, antibody produced by the polyclonal pool of MBC neutralized WT and variant viruses equivalently. Remarkably, we also identified MBC clones that recognized the mutant epitope better than the WT protein, despite never having been exposed to the variant virus. The ability of MBCs to respond to variant viruses in vivo was confirmed by experiments in which MBCs were adoptively transferred or depleted before secondary challenge. Our data demonstrate that class-switched MBC can respond to variants of the original pathogen that escape neutralization of antibody produced by LLPC without a requirement for accumulating additional somatic mutations.
Estimating the voltage-dependent free energy change of ion channels using the median voltage for activation
Authors: Chowdhury Sandipan , Chanda Baron
Published: December 2011

Voltage-gated ion channels are crucial for electrical activity and chemical signaling in a variety of cell types. Structure-activity studies involving electrophysiological characterization of mutants are widely used and allow us to quickly realize the energetic effects of a mutation by measuring macroscopic currents and fitting the observed voltage dependence of conductance to a Boltzmann equation. However, such an approach is somewhat limiting, principally because of the inherent assumption that the channel activation is a two-state process. In this analysis, we show that the area delineated by the gating charge displacement curve and its ordinate axis is related to the free energy of activation of a voltage-gated ion channel. We derive a parameter, the median voltage of charge transfer (Vm), which is proportional to this area, and prove that the chemical component of free energy change of a system can be obtained from the knowledge of Vm and the maximum number of charges transferred. Our method is not constrained by the number or connectivity of intermediate states and is applicable to instances in which the observed responses show a multiphasic behavior. We consider various models of ion channel gating with voltage-dependent steps, latent charge movement, inactivation, etc. and discuss the applicability of this approach in each case. Notably, our method estimates a net free energy change of approximately −14 kcal/mol associated with the full-scale activation of the Shaker potassium channel, in contrast to −2 to −3 kcal/mol estimated from a single Boltzmann fit. Our estimate of the net free energy change in the system is consistent with those derived from detailed kinetic models (Zagotta et al. 1994. J. Gen. Physiol. doi:10.1085/jgp.103.2.321). The median voltage method can reliably quantify the magnitude of free energy change associated with activation of a voltage-dependent system from macroscopic equilibrium measurements. This will be particularly useful in scanning mutagenesis experiments.
The Demons and the Friars: Illicit Magic and Mendicant Rivalry in Renaissance Bologna*
Authors: Herzig Tamar
Published: December 2011

In 1473 Pope Sixtus IV instructed the vicar of the Bishop of Bologna to investigate rumors concerning Carmelite friars who were preaching that summoning demons in order to obtain responses from them was not heretical. Drawing on newly discovered archival sources, this article elucidates the circumstances that led the Franciscan pope to intervene in a conflict between the Bolognese Carmelites and the Dominican inquisitor Simone of Novara. It proposes that the Carmelite affair, which ended with the inquisitor's defeat, constituted a critical juncture in the Dominicans’ relations with other Mendicant orders, and that it shaped inquisitorial activity in Bologna over the next few decades. This paper suggests that the aftermath of the Carmelite affair may also explain why, when the repression of illicit magic was resumed, Inquisitor Giovanni Cagnazzo decided to turn a female necromancer, and not the friars who had taught her demonic rites, into the main target of his prosecution.
Ammonium Secretion During Colletotrichum coccodes Infection Modulates Salicylic and Jasmonic Acid Pathways of Ripe and Unripe Tomato Fruit
Authors: Alkan Noam , Fluhr Robert , Prusky Dov
Published: December 2011

The postharvest pathogens Colletotrichum coccodes remains quiescent after infection of unripe fruit. However, during fruit ripening, the pathogen assumes a necrotrophic life style, rapidly colonizing the tissue. C. coccodes secretes ammonium during germination and colonization of host tissue that induces host programmed cell death. We further examined the role of ammonia in the infection process by analyzing transcriptome expression from infected and ammonia-treated fruit tissue compared with healthy tissue. The analysis revealed 82 and 237 common upregulated and downregulated genes, respectively. Quantitative reverse-transcriptase polymerase chain reaction analysis of select transcripts in normal and transgenic NADPH oxidase antisense plants revealed that their expression was NADPH oxidase dependent. Common-upregulated genes showed overrepresentation of salicylic acid (SA)-dependent genes as well as genes related to biotic stress. The downregulated genes showed overrepresentation of jasmonic acid (JA)-dependent genes. Indeed, direct application of SA to the fruit enhanced C. coccodes necrotrophic colonization, whereas the application of JA delayed colonization. Importantly, green fruit and red fruit displayed similar gene expression patterns although only red fruit is susceptible to colonization. Thus, it is likely that the resistance of green fruit to C. coccodes colonization is due to additional factors.
Cell Individuality: The Bistable Gene Expression of the Type III Secretion System in Dickeya dadantii 3937
Authors: Zeng Quan , Laiosa Michael D. , Steeber Douglas A. , Biddle Eulandria M. , Peng Quan , Yang Ching-Hong
Published: December 2011

Dickeya dadantii 3937 is a gram-negative phytopathogenic bacterium that expresses genes encoding a type III secretion system (T3SS) in a bistable pattern when cultured in a homogeneous minimal media. In this work, we further characterized the bistable gene expression of T3SS at the single-cell level. We demonstrated that bistable expression of the HrpL-regulon genes, such as hrpA and hrpN, is controlled by the same regulatory mechanism. We also showed that the expression level of the T3SS master regulatory gene hrpL plays an important role in the development of the bistable expression of hrpA. A high expression level of hrpL is required but unable to guarantee the high-state expression of hrpA in a cell. In addition, bistable expression patterns of T3SS genes in other gram-negative pathogens of the Enterobacteriaceae and Pseudomonadaceae families were also described in this study. This suggests that the T3SS bistability might be a conserved population behavior in several gram-negative bacterial pathogens.
First Report of Potato spindle tuber viroid in Cape Gooseberry in Slovenia
Authors: Marn M. Viršček , Pleško I. Mavrič
Published: December 2011

Cape gooseberry (Physalis peruviana) was first reported as a host of Potato spindle tuber viroid (PSTVd) in 2009 (4). In Slovenia, 10 young plants of cape gooseberry that were grown in a glasshouse were inspected in April 2011. Plants were multiplied from an adult plant of unknown origin. During sampling, the inspected plants showed no disease symptoms. Total RNA was extracted twice from leaves of five plants with an RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Reverse transcription (RT)-PCR assay employing two pairs of semi-universal pospiviroid primers (Pospi1-RE/FW and Vid-RE/FW [3]) yielded amplicons of the expected size (approximately 196 and 360 bp) from each total RNA preparation. All four DNA products were sequenced directly (Macrogen, Amsterdam, the Netherlands). Sequence analysis confirmed the identity of a viroid as PSTVd. Further RT-PCRs using primer pairs of Shamloul et al. (2) and Di Serio (1) were made to obtain a full viroid sequence. The sequence was deposited in the NCBI GenBank under Accession No. JN543964. Sequence analysis confirmed the identity of the viroid as PSTVd. The Slovenian isolate had 358 nucleotides and was 100% identical to the cape gooseberry isolate from Germany (GenBank Accession No. EU862231) and the tomato isolate from New Zealand (GenBank Accession No. AF369530). The analyzed sample was the only sample of cape gooseberry taken from the start of the survey for PSTVd in 2006 because P. peruviana is rarely grown in Slovenia. To our knowledge, this is the first report of PSTVd infection of P. peruviana in Slovenia and the fourth reported case after the detection of PSTVd infection in Germany, Turkey, and New Zealand. This emerging host for PSTVd could potentially serve as a source of infection for tomato and potato, where the viroid can cause severe losses.

References: (1) F. Di Serio. J. Plant Pathol. 89:297, 2007. (2) A. M. Shamloul et al. Can. J. Plant Pathol. 19:89, 1997. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004. (4) J. Th. J. Verhoeven et al. Plant Dis. 93:316, 2009.
Evaluation of heparanase and matrix metalloproteinase‐9 in patients with cutaneous malignant melanoma
Authors: CHEN Yanhui , CHEN Ying , HUANG Liyong , YU Jianbin
Published: December 2011

Elevated heparanase and matrix metalloproteinase (MMP)‐9, frequently found in human cancer, is a major cause of degradation of the extracellular matrix (ECM) and basement membrane (BM), thus facilitating tumor cell migration and invasion. Although a lot of work has been done, the role of heparanase and MMP‐9 has not been delineated in skin cancer progression. The purpose of this study was to do such an exploration. To investigate the role of heparanase and MMP‐9 in cutaneous malignant melanoma (CMM) development, we performed immunohistochemical analysis to detect the alternation of these two factors in paraffin‐embedded biopsy specimens of normal skin, junctional nevi and CMM. It is interesting to note that the expression profile of heparanase and MMP‐9 was similar. Contrary to negative staining in normal skin, overexpression of heparanase and cytoplasmic MMP‐9 was observed in as many as 70% of CMM, whereas only 10% of the junctional nevi exhibited faint staining (P = 0.0005, P = 0.0000). Considering the lymph node (LN) metastasis, the expression of the two factors is significantly higher in LN‐positive lesions than that in LN‐negative lesions (P = 0.0295, P = 0.0013). Meanwhile, there was positive correlation between the expression of MMP‐9 and heparanase (r = 0.689, P = 0.003). The first expression of MMP‐9 and heparanase occurs at benign lesions. However, the significantly increased expression in advanced CMM stages, particularly in LN‐positive metastasis lesions, might synergistically contribute to degradation of ECM and BM, therefore promoting carcinogenesis and metastasis.
Influence of acute bupropion pre‐treatment on the effects of intranasal cocaine
Authors: Stoops William W. , Lile Joshua A. , Glaser Paul E. A. , Hays Lon R. , Rush Craig R.
Published: December 2011

Aims  The aim of this experiment was to determine the influence of acute bupropion pre‐treatment on subject‐rated effects and choice of intranasal cocaine versus money.

Design  A randomized, within‐subject, placebo‐controlled, double‐blind experiment.

Setting  An out‐patient research unit.

Participants  Eight cocaine‐using adults.

Measurements  Subjects completed nine experimental sessions in which they were pre‐treated with 0, 100 or 200 mg oral immediate release bupropion. Ninety minutes later they sampled an intranasal cocaine dose [4 (placebo), 15 or 45 mg] and made six choices between that dose and an alternative reinforcer (US$0.25), available on independent, concurrent progressive ratio schedules. Subjects also completed a battery of subject‐rated, performance and physiological measures following the sample doses of cocaine.

Findings  After 0 mg bupropion, the high dose of cocaine (45 mg) was chosen five of six times on average compared to 2.25 of six choices for placebo cocaine (4 mg) (P < 0.05). Active bupropion reduced choice of 45 mg cocaine to 3.13 (100 mg) or 4.00 (200 mg) out of six drug choices on average. Bupropion also consistently enhanced positive subject‐rated effects of cocaine (e.g. good effects; willing to take again) while having no effects of its own.

Conclusions  The atypical antidepressant, bupropion, acutely appears to reduce preference for intranasal cocaine versus a small amount of money but to increase reported positive experiences of the drug.
Prevalence and effects of Argemone Mexicana (Papaveraceae) on biodiversity in Ethiopia
Authors: Alemayehu Kefyalew
Published: December 2011

The prevalence and potentials of Argemone mexicana on biodiversity was assessed at Farta, Gondar and Bahir Dar zuria districts. The study areas were stratified into 100 m by 5 m as roadside, fallow land and farmland transect belts. Its effects as poultry feed component were studied on three poultry breeds. Body weights, abnormalities in appetite, egg production and health were recorded. The results indicated that the mean prevalence of Argemone per transect belt in roadside land (17.41 ± 5.9) was higher than that of fallow land (3.35 ± 0.8) and farmland (2.65 ± 0.8) at Farta district. The number and distribution of native plant species under the shed of A. mexicana in roadside, fallow land and farmland per transect belts were 1.15 ± 1.6, 2.25 ± 1.8 and 1.15 ± 0.5, respectively. The number and distribution of Argemone plants in the roadside land per transect increased by 163.4%, 158.5% and 151.9% from 2006 to 2010 in above respective districts. The mean losses in appetite, body weight and egg production were higher in exotic and cross bred than in indigenous chicken ecotypes. Therefore, A. mexicana had negative impacts on biodiversity, native plant species and when used as animal feed components.
MicroRNA‐494 suppresses cell proliferation and induces senescence in A549 lung cancer cells
Authors: Ohdaira H. , Sekiguchi M. , Miyata K. , Yoshida K.
Published: December 2011

Objectives:  MicroRNAs (miRNAs) are small functional RNAs that regulate mRNAs for degradation or translational suppression. In the present study, we aimed to reveal functional importance of miRNA‐494 (miR‐494) in A549 human lung cancer cells.

Materials and methods:  We established A549 cells that constitutively expressed miR‐494. Next, we sought to investigate insulin‐like growth factor 2 mRNA‐binding protein 1 (IGF2BP1) mRNA as an miR‐494 target. For this, we constructed a reporter plasmid bearing potential miR‐494 binding sequences derived from the 3′‐untranslated region (3′‐UTR) of IGF2BP1 mRNA in the 3′‐UTR of the luciferase gene.

Results:  Through comparison between miR‐494 expressing cells and control cells, we revealed that miR‐494 suppressed cell proliferation and colony forming activity, and induced senescence. Reporter activity was inhibited by miR‐494. In addition, IGF2BP1 mRNA levels were down‐regulated in A549 cells that constitutively expressed miR‐494. IGF2BP1 has been shown to bind and suppress IGF2 mRNA, and this could be a reason why IGF2BP1 can regulate cell function. Therefore, we analysed IGF2 mRNA levels and revealed that IGF2 was up‐regulated in A549 cells that constitutively expressed miR‐494. Finally, elevated IGF2 mRNA levels in A549 cells that constitutively expressed miR‐494 were suppressed to basal level by an miR‐494 inhibitor.

Conclusions:  Taken together, IGF2BP1 and its downstream target IGF2 could be a crucial axis for miR‐494 in regulation of the destiny of A549 cells.
Evaluation of kisspeptin levels in obese pregnancy as a biomarker for pre‐eclampsia
Authors: Logie James J. , Denison Fiona C. , Riley Simon C. , Ramaesh Thayalini , Forbes Shareen , Norman Jane E. , Reynolds Rebecca M.
Published: December 2011

Objectives  Circulating concentrations of the peptide kisspeptin have been proposed as a novel biomarker for early detection of pre‐eclampsia. Our aims were to assess analytical and clinical performance characteristics of a commercial kisspeptin assay and to determine sensitivity and specificity of the test for pre‐eclampsia.

Design  Prospective, longitudinal study in a United Kingdom tertiary referral Antenatal Metabolic Clinic.

Patients  Severely obese (body mass index, BMI > 40kg/m2, n = 194) and lean (BMI < 25kg/m2, n = 78) pregnant women.

Measurements  A commercial kisspeptin ELISA (Phoenix Pharmaceuticals) was assessed for analytical sensitivity, specificity, precision, linearity, recovery and stability in maternal plasma samples at 16, 28 and 36 weeks gestation. Pre‐eclampsia, defined using International Society for the Study of Hypertension in Pregnancy guidelines; blood pressure; delivery gestation; birthweight.

Results  Kisspeptin concentrations were lower in early pregnancy in obese women (P < 0·001), and in women who later developed pre‐eclampsia (P < 0·05), compared with women with uncomplicated pregnancies. For 16‐week plasma kisspeptin in prediction of pre‐eclampsia, area under the receiver‐operator characteristic curve was 0·80 (P < 0·01), positive and negative likelihood ratios were 3·0 and 0·2, and test sensitivity and specificity were 85·7 and 71·4%, respectively. In regression analyses, kisspeptin (16 weeks) associated positively with delivery gestation (P < 0·05) and birthweight (P < 0·0001), and negatively with 28‐ and 36‐week blood pressure (P < 0·0001).

Conclusions  Kisspeptin concentration in early pregnancy is a promising biomarker for pre‐eclampsia and low birthweight but cannot be recommended, in isolation, for universal screening because of inadequate test sensitivity and specificity. Large‐scale studies are required to assess its potential in a panel of biomarkers.