bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant diversity effects on soil food webs are stronger than those of elevated CO
2
and N deposition in a long-term grassland experiment
Authors: Eisenhauer Nico , Dobies Tomasz , Cesarz Simone , Hobbie Sarah E. , Meyer Ross J. , Worm Kally , Reich Peter B.
Published: April 2013

Recent metaanalyses suggest biodiversity loss affects the functioning of ecosystems to a similar extent as other global environmental change agents. However, the abundance and functioning of soil organisms have been hypothesized to be much less responsive to such changes, particularly in plant diversity, than aboveground variables, although tests of this hypothesis are extremely rare. We examined the responses of soil food webs (soil microorganisms, nematodes, microarthropods) to 13-y manipulation of multiple environmental factors that are changing at global scales—specifically plant species richness, atmospheric CO
2
, and N deposition—in a grassland experiment in Minnesota. Plant diversity was a strong driver of the structure and functioning of soil food webs through several bottom-up (resource control) effects, whereas CO
2
and N only had modest effects. We found few interactions between plant diversity and CO
2
and N, likely because of weak interactive effects of those factors on resource availability (e.g., root biomass). Plant diversity effects likely were large because high plant diversity promoted the accumulation of soil organic matter in the site’s sandy, organic matter–poor soils. Plant diversity effects were not explained by the presence of certain plant functional groups. Our results underline the prime importance of plant diversity loss cascading to soil food webs (density and diversity of soil organisms) and functions. Because the present results suggest prevailing plant diversity effects and few interactions with other global change drivers, protecting plant diversity may be of high priority to maintain the biodiversity and functioning of soils in a changing world.
Synthetic microRNA-mediated downregulation of Nogo-A in transgenic rats reveals its role as regulator of synaptic plasticity and cognitive function
Authors: Tews Björn , Schönig Kai , Arzt Michael E. , Clementi Stefano , Rioult-Pedotti Mengia-Seraina , Zemmar Ajmal , Berger Stefan M. , Schneider Miriam , Enkel Thomas , Weinmann Oliver , Kasper Hansjörg , Schwab Martin E. , Bartsch Dusan
Published: April 2013

We have generated a transgenic rat model using RNAi and used it to study the role of the membrane protein Nogo-A in synaptic plasticity and cognition. The membrane protein Nogo-A is expressed in CNS oligodendrocytes and subpopulations of neurons, and it is known to suppress neurite growth and regeneration. The constitutively expressed polymerase II-driven transgene was composed of a microRNA-targeting Nogo-A placed into an intron preceding the coding sequence for EGFP, thus quantitatively labeling cells according to intracellular microRNA expression. The transgenic microRNA in vivo efficiently reduced the concentration of Nogo-A mRNA and protein preferentially in neurons. The resulting significant increase in long-term potentiation in both hippocampus and motor cortex indicates a repressor function of Nogo-A in synaptic plasticity. The transgenic rats exhibited prominent schizophrenia-like behavioral phenotypes, such as perseveration, disrupted prepulse inhibition, and strong withdrawal from social interactions. This fast and efficient microRNA-mediated knockdown provides a way to silence gene expression in vivo in transgenic rats and shows a role of Nogo-A in regulating higher cognitive brain functions.
Surface wettability plays a significant role in gecko adhesion underwater
Authors: Stark Alyssa Y. , Badge Ila , Wucinich Nicholas A. , Sullivan Timothy W. , Niewiarowski Peter H. , Dhinojwala Ali
Published: April 2013

Although we now have thousands of studies focused on the nano-, micro-, and whole-animal mechanics of gecko adhesion on clean, dry substrates, we know relatively little about the effects of water on gecko adhesion. For many gecko species, however, rainfall frequently wets the natural surfaces they navigate. In an effort to begin closing this gap, we tested the adhesion of geckos on submerged substrates that vary in their wettability. When tested on a wet hydrophilic surface, geckos produced a significantly lower shear adhesive force (5.4 ± 1.33 N) compared with a dry hydrophilic surface (17.1 ± 3.93 N). In tests on an intermediate wetting surface and a hydrophobic surface, we found no difference in shear adhesion between dry and wet contact. Finally, in tests on polytetrafluoroethylene (PTFE), we found that geckos clung significantly better to wet PTFE (8.0 ± 1.09 N) than dry PTFE (1.6 ± 0.66 N). To help explain our results, we developed models based on thermodynamic theory of adhesion for contacting surfaces in different media and found that we can predict the ratio of shear adhesion in water to that in air. Our findings provide insight into how geckos may function in wet environments and also have significant implications for the development of a synthetic gecko mimic that retains adhesion in water.
Inducible deletion of the Blimp-1 gene in adult epidermis causes granulocyte-dominated chronic skin inflammation in mice
Authors: Chiang Ming-Feng , Yang Shii-Yi , Lin I-Ying , Hong Jin-Bon , Lin Sung-Jan , Ying Hsia-Yuan , Chen Chun-Ming , Wu Shih-Ying , Liu Fu-Tong , Lin Kuo-I
Published: April 2013

B lymphocyte-induced maturation protein-1 (Blimp-1) is a transcriptional repressor important for the differentiation and function of several types of immune cells. Because skin serves as a physical barrier and acts as an immune sentinel, we investigated whether Blimp-1 is involved in epidermal immune function. We show that Blimp-1 expression is reduced in skin lesions of some human eczema samples and in stimulated primary keratinocytes. Epidermal-specific deletion of PR domain containing 1, with ZNF domain (
Prdm1
), the gene encoding Blimp-1, in adult mice caused spontaneously inflamed skin characterized by massive dermal infiltration of neutrophils/macrophages and development of chronic inflammation associated with higher levels of cytokines/chemokines, including granulocyte colony-stimulating factor (G-CSF), and enhanced myelopoiesis in bone marrow. Deletion of
Prdm1
in the epidermis of adult mice also led to stronger inflammatory reactions in a tape-stripping test and in a disease model of contact dermatitis. The elevated G-CSF produced by keratinocytes after deletion of
Prdm1
in vitro was mediated by the transcriptional activation of FBJ osteosarcoma oncogene (
Fos
) and fos-like antigen 1 (
Fosl1
). Systemic increases in G-CSF contributed to the inflammatory responses, because deletion of the G-CSF gene [colony stimulating factor 3, (
Csf3
)] prevented neutrophilia and partially ameliorated the inflamed skin in
Prdm1-
deficient mice. Our findings indicate a previously unreported function for Blimp-1 in restraining steady-state epidermal barrier immunity.
Influence of multiple dam passage on survival of juvenile Chinook salmon in the Columbia River estuary and coastal ocean
Authors: Rechisky Erin L. , Welch David W. , Porter Aswea D. , Jacobs-Scott Melinda C. , Winchell Paul M.
Published: April 2013

Multiple dam passage during seaward migration is thought to reduce the subsequent survival of Snake River Chinook salmon. This hypothesis developed because juvenile Chinook salmon from the Snake River, the Columbia River’s largest tributary, migrate >700 km through eight hydropower dams and have lower adult return rates than downstream populations that migrate through only 3 or 4 dams. Using a large-scale telemetry array, we tested whether survival of hatchery-reared juvenile Snake River spring Chinook salmon is reduced in the estuary and coastal ocean relative to a downstream, hatchery-reared population from the Yakima River. During the initial 750-km, 1-mo-long migration through the estuary and coastal ocean, we found no evidence of differential survival; therefore, poorer adult returns of Snake River Chinook may develop far from the Columbia River. Thus, hydrosystem mitigation efforts may be ineffective if differential mortality rates develop in the North Pacific Ocean for reasons unrelated to dam passage.
Ammonia oxidation pathways and nitrifier denitrification are significant sources of N
2
O and NO under low oxygen availability
Authors: Zhu Xia , Burger Martin , Doane Timothy A. , Horwath William R.
Published: April 2013

The continuous increase of nitrous oxide (N
2
O) abundance in the atmosphere is a global concern. Multiple pathways of N
2
O production occur in soil, but their significance and dependence on oxygen (O
2
) availability and nitrogen (N) fertilizer source are poorly understood. We examined N
2
O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O
2
concentrations following urea or ammonium sulfate [(NH
4
)
2
SO
4
] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH
3
) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N
2
O production was determined in 36-h incubations in microcosms by
15
N-
18
O isotope and NH
3
oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH
3
oxidation pathways increased as O
2
concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O
2
concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N
2
O production. Heterotrophic denitrification was responsible for all N
2
O production at 0% O
2
. Nitrifier denitrification was the main source of N
2
O production from ammonical fertilizer under low O
2
concentrations with urea producing more N
2
O than (NH
4
)
2
SO
4
additions. These findings challenge established thought attributing N
2
O emissions from soils with high water content to HD due to presumably low O
2
availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N
2
O production in agricultural soils.
Rate enhancement of bacterial extracellular electron transport involves bound flavin semiquinones
Authors: Okamoto Akihiro , Hashimoto Kazuhito , Nealson Kenneth H. , Nakamura Ryuhei
Published: April 2013

Extracellular redox-active compounds, flavins and other quinones, have been hypothesized to play a major role in the delivery of electrons from cellular metabolic systems to extracellular insoluble substrates by a diffusion-based shuttling two-electron-transfer mechanism. Here we show that flavin molecules secreted by
Shewanella oneidensis
MR-1 enhance the ability of its outer-membrane
c
-type cytochromes (OM
c-
Cyts) to transport electrons as redox cofactors, but not free-form flavins. Whole-cell differential pulse voltammetry revealed that the redox potential of flavin was reversibly shifted more than 100 mV in a positive direction, in good agreement with increasing microbial current generation. Importantly, this flavin/OM
c-
Cyts interaction was found to facilitate a one-electron redox reaction via a semiquinone, resulting in a 10
3
- to 10
5
-fold faster reaction rate than that of free flavin. These results are not consistent with previously proposed redox-shuttling mechanisms but suggest that the flavin/OM
c-
Cyts interaction regulates the extent of extracellular electron transport coupled with intracellular metabolic activity.
Interpolated memory tests reduce mind wandering and improve learning of online lectures
Authors: Szpunar Karl K. , Khan Novall Y. , Schacter Daniel L.
Published: April 2013

The recent emergence and popularity of online educational resources brings with it challenges for educators to optimize the dissemination of online content. Here we provide evidence that points toward a solution for the difficulty that students frequently report in sustaining attention to online lectures over extended periods. In two experiments, we demonstrate that the simple act of interpolating online lectures with memory tests can help students sustain attention to lecture content in a manner that discourages task-irrelevant mind wandering activities, encourages task-relevant note-taking activities, and improves learning. Importantly, frequent testing was associated with reduced anxiety toward a final cumulative test and also with reductions in subjective estimates of cognitive demand. Our findings suggest a potentially key role for interpolated testing in the development and dissemination of online educational content.
Characterization of mechanical and biochemical properties of developing embryonic tendon
Authors: Marturano Joseph E. , Arena Jeffrey D. , Schiller Zachary A. , Georgakoudi Irene , Kuo Catherine K.
Published: April 2013

Tendons have uniquely high tensile strength, critical to their function to transfer force from muscle to bone. When injured, their innate healing response results in aberrant matrix organization and functional properties. Efforts to regenerate tendon are challenged by limited understanding of its normal development. Consequently, there are few known markers to assess tendon formation and parameters to design tissue engineering scaffolds. We profiled mechanical and biological properties of embryonic tendon and demonstrated functional properties of developing tendon are not wholly reflected by protein expression and tissue morphology. Using force volume-atomic force microscopy, we found that nano- and microscale tendon elastic moduli increase nonlinearly and become increasingly spatially heterogeneous during embryonic development. When we analyzed potential biochemical contributors to modulus, we found statistically significant but weak correlation between elastic modulus and collagen content, and no correlation with DNA or glycosaminoglycan content, indicating there are additional contributors to mechanical properties. To investigate collagen cross-linking as a potential contributor, we inhibited lysyl oxidase-mediated collagen cross-linking, which significantly reduced tendon elastic modulus without affecting collagen morphology or DNA, glycosaminoglycan, and collagen content. This suggests that lysyl oxidase-mediated cross-linking plays a significant role in the development of embryonic tendon functional properties and demonstrates that changes in cross-links alter mechanical properties without affecting matrix content and organization. Taken together, these data demonstrate the importance of functional markers to assess tendon development and provide a profile of tenogenic mechanical properties that may be implemented in tissue engineering scaffold design to mechanoregulate new tendon regeneration.
Bone marrow injection stimulates hepatic ductular reactions in the absence of injury via macrophage-mediated TWEAK signaling
Authors: Bird Thomas G. , Lu Wei-Yu , Boulter Luke , Gordon-Keylock Sabrina , Ridgway Rachel A. , Williams Michael J. , Taube Jessica , Thomas James A. , Wojtacha Davina , Gambardella Adriana , Sansom Owen J. , Iredale John P. , Forbes Stuart J.
Published: April 2013

Tissue progenitor cells are an attractive target for regenerative therapy. In various organs, bone marrow cell (BMC) therapy has shown promising preliminary results, but to date no definite mechanism has been demonstrated to account for the observed benefit in organ regeneration. Tissue injury and regeneration is invariably accompanied by macrophage infiltration, but their influence upon the progenitor cells is incompletely understood, and direct signaling pathways may be obscured by the multiple roles of macrophages during organ injury. We therefore examined a model without injury; a single i.v. injection of unfractionated BMCs in healthy mice. This induced ductular reactions (DRs) in healthy mice. We demonstrate that macrophages within the unfractionated BMCs are responsible for the production of DRs, engrafting in the recipient liver and localizing to the DRs. Engrafted macrophages produce the cytokine TWEAK (TNF-like weak inducer of apoptosis) in situ. We go on to show that recombinant TWEAK activates DRs and that BMC mediated DRs are TWEAK dependent. DRs are accompanied by liver growth, occur in the absence of liver tissue injury and hepatic progenitor cells can be isolated from the livers of mice with DRs. Overall these results reveal a hitherto undescribed mechanism linking macrophage infiltration to DRs in the liver and highlight a rationale for macrophage derived cell therapy in regenerative medicine.
Memory reconsolidation and its maintenance depend on L-voltage-dependent calcium channels and CaMKII functions regulating protein turnover in the hippocampus
Authors: Da Silva Weber Cláudio , Cardoso Gabriela , Bonini Juliana Sartori , Benetti Fernando , Izquierdo Ivan
Published: April 2013

Immediate postretrieval bilateral blockade of long-acting voltage–dependent calcium channels (L-VDCCs), but not of glutamatergic NMDA receptors, in the dorsal CA1 region of the hippocampus hinders retention of long-term spatial memory in the Morris water maze. Immediate postretrieval bilateral inhibition of calcium/calmodulin-dependent protein kinase (CaMK) II in dorsal CA1 does not affect retention of this task 24 h later but does hinder it 5 d later. These two distinct amnesic effects are abolished if protein degradation by proteasomes is inhibited concomitantly. These results indicate that spatial memory reconsolidation depends on the functionality of L-VDCC in dorsal CA1, that maintenance of subsequent reconsolidated memory trace depends on CaMKII, and these results also suggest that the role played by both L-VDCC and CaMKII is to promote the retrieval-dependent, synaptically localized enhancement of protein synthesis necessary to counteract a retrieval-dependent, synaptic-localized enhancement of protein degradation, which has been described as underlying the characteristic labilization of the memory trace triggered by retrieval. Thus, conceivably, L-VDCC and CaMKII would enhance activity-dependent localized protein renewal, which may account for the improvement of the long-term efficiency of the synapses responsible for the maintenance of reactivated long-term spatial memory.
Signs of critical transition in the Everglades wetlands in response to climate and anthropogenic changes
Authors: Foti Romano , del Jesus Manuel , Rinaldo Andrea , Rodriguez-Iturbe Ignacio
Published: April 2013

The increasing pressure of climatic change and anthropogenic activities is predicted to have major effects on ecosystems around the world. With their fragility and sensitivity to hydrologic shifts and land-use changes, wetlands are among the most vulnerable of such ecosystems. Focusing on the Everglades National Park, we here assess the impact of changes in the hydrologic regime, as well as habitat loss, on the spatial configuration of vegetation species. Because the current structuring of vegetation clusters in the Everglades exhibits power-law behavior and such behavior is often associated with self-organization and dynamics occurring near critical transition points, the quantification and prediction of the impact of those changes on the ecosystem is deemed of paramount importance. We implement a robust model able to identify the main hydrologic and local drivers of the vegetation species spatial structuring and apply it for quantitative assessment. We find that shifts in the hydropatterns will mostly affect the relative abundance of species that currently colonize specific hydroperiod niches. Habitat loss or disruption, however, would have a massive impact on all plant communities, which are found to exhibit clear threshold behaviors when a given percentage of habitable habitat is lost.
Diversity and heritability of the maize rhizosphere microbiome under field conditions
Authors: Peiffer Jason A. , Spor Aymé , Koren Omry , Jin Zhao , Tringe Susannah Green , Dangl Jeffery L. , Buckler Edward S. , Ley Ruth E.
Published: April 2013

The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant–microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding.
Unique drug screening approach for prion diseases identifies tacrolimus and astemizole as antiprion agents
Authors: Karapetyan Yervand Eduard , Sferrazza Gian Franco , Zhou Minghai , Ottenberg Gregory , Spicer Timothy , Chase Peter , Fallahi Mohammad , Hodder Peter , Weissmann Charles , Lasmézas Corinne Ida
Published: April 2013

Prion diseases such as Creutzfeldt–Jakob disease (CJD) are incurable and rapidly fatal neurodegenerative diseases. Because prion protein (PrP) is necessary for prion replication but dispensable for the host, we developed the PrP–FRET-enabled high throughput assay (PrP–FEHTA) to screen for compounds that decrease PrP expression. We screened a collection of drugs approved for human use and identified astemizole and tacrolimus, which reduced cell-surface PrP and inhibited prion replication in neuroblastoma cells. Tacrolimus reduced total cellular PrP levels by a nontranscriptional mechanism. Astemizole stimulated autophagy, a hitherto unreported mode of action for this pharmacophore. Astemizole, but not tacrolimus, prolonged the survival time of prion-infected mice. Astemizole is used in humans to treat seasonal allergic rhinitis in a chronic setting. Given the absence of any treatment option for CJD patients and the favorable drug characteristics of astemizole, including its ability to cross the blood–brain barrier, it may be considered as therapy for CJD patients and for prophylactic use in familial prion diseases. Importantly, our results validate PrP-FEHTA as a method to identify antiprion compounds and, more generally, FEHTA as a unique drug discovery platform.
Identification of a dimerization domain in the TMEM16A calcium-activated chloride channel (CaCC)
Authors: Tien Jason , Lee Hye Young , Minor Daniel L. , Jan Yuh Nung , Jan Lily Yeh
Published: April 2013

Transmembrane proteins with unknown function 16 (TMEM16A) is a calcium-activated chloride channel (CaCC) important for neuronal, exocrine, and smooth muscle functions. TMEM16A belongs to a family of integral membrane proteins that includes another CaCC, TMEM16B, responsible for controlling action potential waveform and synaptic efficacy, and a small-conductance calcium-activated nonselective cation channel, TMEM16F, linked to Scott syndrome. We find that these channels in the TMEM16 family share a homodimeric architecture facilitated by their cytoplasmic N termini. This dimerization domain is important for channel assembly in eukaryotic cells, and the in vitro association of peptides containing the dimerization domain is consistent with a homotypic protein–protein interaction. Amino acid substitutions in the dimerization domain affect functional TMEM16A-CaCC channel expression, as expected from its critical role in channel subunit assembly.
Anomalous heat transport and condensation in convection of cryogenic helium
Authors: Urban Pavel , Schmoranzer David , Hanzelka Pavel , Sreenivasan Katepalli R. , Skrbek Ladislav
Published: April 2013

When a hot body A is thermally connected to a cold body B, the textbook knowledge is that heat flows from A to B. Here, we describe the opposite case in which heat flows from a colder but constantly heated body B to a hotter but constantly cooled body A through a two-phase liquid–vapor system. Specifically, we provide experimental evidence that heat flows through liquid and vapor phases of cryogenic helium from the constantly heated, but cooler, bottom plate of a Rayleigh–Bénard convection cell to its hotter, but constantly cooled, top plate. The bottom plate is heated uniformly, and the top plate is cooled by heat exchange with liquid helium maintained at 4.2 K. Additionally, for certain experimental conditions, a rain of helium droplets is detected by small sensors placed in the cell at about one-half of its height.
Nuclear resonance vibrational spectroscopic and computational study of high-valent diiron complexes relevant to enzyme intermediates
Authors: Park Kiyoung , Bell Caleb B. , Liu Lei V. , Wang Dong , Xue Genqiang , Kwak Yeonju , Wong Shaun D. , Light Kenneth M. , Zhao Jiyong , Alp E. Ercan , Yoda Yoshitaka , Saito Makina , Kobayashi Yasuhiro , Ohta Takehiro , Seto Makoto , Que Lawrence , Solomon Edward I.
Published: April 2013

High-valent intermediates of binuclear nonheme iron enzymes are structurally unknown despite their importance for understanding enzyme reactivity. Nuclear resonance vibrational spectroscopy combined with density functional theory calculations has been applied to structurally well-characterized high-valent mono- and di-oxo bridged binuclear Fe model complexes. Low-frequency vibrational modes of these high-valent diiron complexes involving Fe motion have been observed and assigned. These are independent of Fe oxidation state and show a strong dependence on spin state. It is important to note that they are sensitive to the nature of the Fe
2
core bridges and provide the basis for interpreting parallel nuclear resonance vibrational spectroscopy data on the high-valent oxo intermediates in the binuclear nonheme iron enzymes.
Fairy tales, landscapes and metaphor in supervision: An exploratory study
Authors: Smith Margaret E. , Bird Drew
Published: April 2013

Objective: Supervision is an important requirement for most health professionals and finding innovative and creative forms of ensuring safe and ethical practice are helpful to practitioners. This paper explores the use of fairy tales, mental landscapes and metaphors to illuminate the therapeutic and supervisory relationship. A therapy case study was used as reference. Design: The design was based on a grounded theory methodology and qualitative‐based collaborative meetings between professionals. Both researchers/participants were from different therapeutic backgrounds; drama therapy and integrative counselling. Findings: Two main themes emerged relating to the therapeutic process: (1) Using Archetypal themes in fairy tales to enhance the clarity of the therapeutic landscape; and (2) The facilitation of the sense system through the use of small objects to reconceptualise the therapeutic dynamic. Conclusion: The use of metaphor and small objects to explore retrospective therapeutic encounters can enhance the role of supervision by broadening the cognitive landscape of the therapist. Implications for the therapist/client and supervisor relationships are considered.
Alternative Feeding Strategies to Maximize Fish Oil and Fish Meal Sparing in Largemouth Bass Culture while Maintaining Production Performance and Product Value
Authors: Coursey Andrew R , Trushenski Jesse T , Kohler Christopher C
Published: April 2013

Feeding trials were conducted to determine (1) the optimal inclusion of poultry byproduct meal (PBM) and poultry fat (PF) as alternatives to fish meal (FM) and fish oil (FO) in diets for Largemouth Bass Micropterus salmoides and (2) whether the poultry-based formulations could be used in conjunction with FO-based finishing feeds in a strategy to minimize the use of marine-derived ingredients while maintaining performance and fillet composition. In trial 1, fish (mean ± SE = 16.0 ± 0.5 g) were reared for 9 weeks on diets (∼40% protein, ∼10% lipid) containing graded levels of FM (0, 7.5, or 15%) and FO (0, 3, or 6%), with PBM and PF replacing FM and FO, respectively. The results indicated that complete replacement of marine feedstuffs with PBM and PF had no significant effects on production performance; all diets yielded equivalent weight gain (mean ± SE = 277 ± 45%), feed conversion ratio (FCR; 1.4 ± 0.4), and feed consumption (39 ± 6 g/fish), although fillet fatty acid profile reflected the diet. Based on these results, the 7.5% FM–0% FO and 0% FM–0% FO diets were further evaluated. In trial 2, fish (mean ± SE = 39 ± 3 g) were reared for 16 weeks on the 7.5% FM–0% FO or 0% FM–0% FO feeds, followed by an additional 12 weeks on the assigned diet or a 15% FM–6% FO finishing diet. The performance and fillet composition of these fish were compared with those of their counterparts that only received the finishing feed or a commercially available Largemouth Bass feed. All approaches yielded equivalent weight gain (mean ± SE = 496 ± 65%), FCR (2.0 ± 0.2), and feed consumption (407 ± 65 g/fish). Fillet fatty acid profiles reflected dietary intake, but finishing significantly increased the n-3 fatty acid and long-chain polyunsaturated fatty acid levels. The use of poultry-byproduct-based Largemouth Bass feeds may offer cost savings, and undesired effects on fillet nutritional value may be attenuated by the use of finishing feeds.
Saturated Fatty Acids Limit the Effects of Replacing Fish Oil with Soybean Oil with or without Phospholipid Supplementation in Feeds for Juvenile Cobia
Authors: Trushenski Jesse , Woitel Franklin , Schwarz Michael , Yamamoto Fernando
Published: April 2013

The high cost and limited availability of fish oil makes plant-derived lipids attractive for aquafeed manufacturing, but replacing fish oil with these lipids can result in long-chain polyunsaturated fatty acid (LC-PUFA) deficiencies. Fatty acid metabolism, specifically the efficiency of LC-PUFA utilization, may be influenced by the dietary saturated fatty acid (SFA) content versus that of C18 polyunsaturated fatty acids (PUFAs). We assessed the growth and tissue composition of Cobia Rachycentron canadum (55.3 ± 0.2 g initial weight [mean ± SE]; 10 fish/tank, 3 tanks/diet) fed diets (∼49% protein, ∼10% lipid) containing fish oil; 22:6(n-3)–amended standard, partially hydrogenated, or fully hydrogenated soybean oil; and these same soybean oils supplemented with soybean lecithin for 8 weeks. Although survival (range = 97–100%), final weight (160–189 g), and feed conversion ratio (1.40–1.52) were unaffected by diet, differences were observed in weight gain (185–241%), specific growth rate (1.87–2.19% body weight/d), and feed intake (2.94–3.44% body weight/d). Significant effects of soybean oil type on final weight, weight gain, feed conversion ratio, specific growth rate, and feed intake were noted, with standard soybean oil generally outperforming the other soybean lipids when oil types were pooled across phospholipid supplementation treatments, whereas phospholipid supplementation had no significant effect on any of the performance measures. Differences in dietary fatty acid profile yielded differences in tissue composition. Feeding standard soybean oil resulted in the most greatly modified profiles, whereas the profiles of fish fed fully hydrogenated, completely saturated soybean oil were most similar to those of the fish oil–fed fish. The magnitude of profile change was greatest in the liver and fillet tissues and smallest in the eye and brain tissues. Although further research is necessary to demonstrate whether SFA-rich lipids can effectively reduce the LC-PUFA requirements of Cobia, it is clear that SFA-rich oils offer a strategic advantage in minimizing the effects of fish oil replacement on tissue fatty acid profile.
On almost-Fuchsian manifolds
Authors: Huang Zheng , Wang Biao
Published: April 2013

An almost-Fuchsian manifold is a class of complete hyperbolic three-manifolds. Such a three-manifold is a quasi-Fuchsian manifold which contains a closed incompressible minimal surface with principal curvatures everywhere in the range of(−1,1)(-1,1). In such a manifold, the minimal surface is unique and embedded, hence one can parametrize these hyperbolic three-manifolds by their minimal surfaces. In this paper we obtain estimates on several geometric and analytical quantities of an almost-Fuchsian manifoldMMin terms of the data on the minimal surface. In particular, we obtain an upper bound for the hyperbolic volume of the convex core ofMMand an upper bound on the Hausdorff dimension of the limit set associated toMM. We also constructed a quasi-Fuchsian manifold which admits more than one minimal surface, and it does not admit a foliation of closed surfaces of constant mean curvature.
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways
Authors: Fried Jake Y. , van Iersel Martijn P. , Aladjem Mirit I. , Kohn Kurt W. , Luna Augustin
Published: April 2013

Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries.

Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License.

Contact:  augustin@mail.nih.gov or jakeyfried@gmail.com
ThedarGenes ofPseudomonas chlororaphisPCL1606 Are Crucial for Biocontrol Activity via Production of the Antifungal Compound 2-Hexyl, 5-Propyl Resorcinol
Authors: Calderón Claudia E. , Pérez-García Alejandro , de Vicente Antonio , Cazorla Francisco M.
Published: April 2013

To determine the genetic basis by which 2-hexyl, 5-propyl resorcinol (HPR) is produced by the biocontrol rhizobacterium Pseudomonas chlororaphis (formerly known as P. fluorescens) PCL1606, the presence and role of dar genes were investigated. To accomplish this aim, the pCGNOV-1 plasmid was isolated from a PCL1606 genomic library and was shown to hybridize to various dar probes by Southern blot. An analysis of the pCGNOV-1 genomic DNA revealed the presence of five open reading frames that were homologous to dar genes and had an organization that resembled the arrangement of previously described P. chlororaphis strains. Phylogenetic studies resulted in the clustering of PCL1606 with the P. chlororaphis subgroup, which supported the renaming of this strain from P. fluorescens to P. chlororaphis PCL1606. The construction of insertional mutants for each homologous dar gene in P. chlororaphis PCL1606 along with their corresponding complemented derivative strains restored HPR production and confirmed the key role of the dar A and darB genes in HPR production and in the antagonistic phenotype. Finally, biocontrol assays were performed on avocado–Rosellinia and tomato–Fusarium test systems using the HPR-defective and -complemented derivative strains generated here and demonstrated the crucial role of the biosynthetic dar genes in the biocontrol phenotype of P. chlororaphis PCL1606. This biocontrol phenotype is dependent on the dar genes via their production of the HPR antibiotic. Some of the dar genes not directly involved in the biosynthesis of HPR, such as darS or darR, might contribute to regulatory features of HPR production.
Placement of an Intrathecal Catheter Through a Bony Fusion Mass Using 3D Image Guidance
Authors: Candler Shawn A. , Osborne Michael D. , Derr Michael J. , Nottmeier Eric W.
Published: April 2013

Objective:

We describe the 3-dimensional (3D) image-guided placement technique for a lumbar intrathecal catheter through a dorsal fusion mass. This is the first time this technique has been reported. A patient with 6 prior spine surgeries and chronic pain syndrome presented with a challenging large dorsal fusion mass. The use of 3D cone beam computed tomography–based image guidance proved advantageous for the placement of an intrathecal drug delivery system (IDDS).

Method:

Under general anesthesia, image guidance was accomplished with the Medtronic Stealth S7 image guidance system, used in conjunction with the O-ARM (Medtronic Inc.). Using an image-guided probe over the skin surface, we navigated the dorsal fusion mass to identify a thin area at the L4-L5 level. A small incision was made and the image-guided probe was used to target the selected thin area and drill an adequate opening in the fusion mass. We inserted a Tuohy needle through the bony defect for passage of the intrathecal catheter. We confirmed adequate catheter placement using free flowing cerebrospinal fluid and fluoroscopy. The remainder of the IDDS implant proceeded per routine.

Results:

The patient tolerated the procedure well and had no complications. The morphine IDDS improved his overall pain and function with minimal side effects.

Conclusions:

This is the first case report using 3D cone beam computed tomography–based image guidance for the placement of an intrathecal catheter through a bony fusion mass. This technique appears to be a viable option for IDDS implantation in patients with difficult anatomy.
Fecal S100A12
Authors: Däbritz Jan , Foell Dirk , Wirth Stefan , Jenke Andreas
Published: April 2013

Objectives:

The aim of the study was to determine whether longitudinal measurements of fecal S100A12, a damage‐associated molecular pattern protein, which is released from neutrophils or monocytes under stress, can detect very‐low‐birth‐weight (VLBW) infants at risk for intestinal distress apart from necrotizing enterocolitis.

Methods:

This prospective study included 46 VLBW infants with intestinal distress and 49 reference patients. Meconium and stool samples were collected prospectively on alternate days for 4 weeks, and fecal S100A12 was measured by enzyme‐linked immunosorbent assay.

Results:

Gestational age and weight at birth were significantly lower in patients with intestinal distress when compared to unaffected reference infants. Median levels of fecal S100A12 were significantly higher in patients with intestinal distress at onset of disease and before compared with unaffected reference infants. Median levels of fecal S100A12 declined steadily to baseline levels within 2 weeks after disease onset. The ideal cutoff value for identifying patients with intestinal distress within 7 days before disease onset was 60 μg/kg (sensitivity 0.73; specificity 0.55).

Conclusions:

Fecal S100A12 levels are increased in VLBW infants with intestinal distress; however, the potential for S100A12 as an early biomarker is largely limited by overlaps between values of infants with intestinal distress and the reference population.
Some existence results on nonlinear fractional differential equations
Authors: Baleanu Dumitru , Rezapour Shahram , Mohammadi Hakimeh
Published: April 2013

In this paper, by using fixed-point methods, we study the existence and uniqueness of a solution for the nonlinear fractional differential equation boundary-value problem
D

α

u
(
t
)=
f
(
t
,
u
(
t
)) with a Riemann–Liouville fractional derivative via the different boundary-value problems
u
(0)=
u
(
T
), and the three-point boundary condition
u
(0)=
β
1
u
(
η
) and
u
(
T
)=
β
2
u
(
η
), where
T
>0,
t
∈
I
=[0,
T
], 0<
α
<1, 0<
η
<
T
, 0<
β
1
<
β
2
<1.
Fractional-order variational optical flow model for motion estimation
Authors: Chen Dali , Sheng Hu , Chen YangQuan , Xue Dingyü
Published: April 2013

A new class of fractional-order variational optical flow models, which generalizes the differential of optical flow from integer order to fractional order, is proposed for motion estimation in this paper. The corresponding Euler–Lagrange equations are derived by solving a typical fractional variational problem, and the numerical implementation based on the Grünwald–Letnikov fractional derivative definition is proposed to solve these complicated fractional partial differential equations. Theoretical analysis reveals that the proposed fractional-order variational optical flow model is the generalization of the typical Horn and Schunck (first-order) variational optical flow model and the second-order variational optical flow model, which provides a new idea for us to study the optical flow model and has an important theoretical implication in optical flow model research. The experiments demonstrate the validity of the generalization of differential order.
Stability and convergence of an implicit numerical method for the space and time fractional Bloch–Torrey equation
Authors: Yu Qiang , Liu Fawang , Turner Ian , Burrage Kevin
Published: April 2013

Fractional-order dynamics in physics, particularly when applied to diffusion, leads to an extension of the concept of Brownian motion through a generalization of the Gaussian probability function to what is termed anomalous diffusion. As magnetic resonance imaging is applied with increasing temporal and spatial resolution, the spin dynamics is being examined more closely; such examinations extend our knowledge of biological materials through a detailed analysis of relaxation time distribution and water diffusion heterogeneity. Here, the dynamic models become more complex as they attempt to correlate new data with a multiplicity of tissue compartments, where processes are often anisotropic. Anomalous diffusion in the human brain using fractional-order calculus has been investigated. Recently, a new diffusion model was proposed by solving the Bloch–Torrey equation using fractional-order calculus with respect to time and space. However, effective numerical methods and supporting error analyses for the fractional Bloch–Torrey equation are still limited. In this paper, the space and time fractional Bloch–Torrey equation (ST-FBTE) in both fractional Laplacian and Riesz derivative form is considered. The time and space derivatives in the ST-FBTE are replaced by the Caputo and the sequential Riesz fractional derivatives, respectively. Firstly, we derive an analytical solution for the ST-FBTE in fractional Laplacian form with initial and boundary conditions on a finite domain. Secondly, we propose an implicit numerical method (INM) for the ST-FBTE based on the Riesz form, and the stability and convergence of the INM are investigated. We prove that the INM for the ST-FBTE is unconditionally stable and convergent. Finally, we present some numerical results that support our theoretical analysis.
Veratrole Biosynthesis in White Campion
Authors: Akhtar Tariq A. , Pichersky Eran
Published: April 2013

White campion (Silene latifolia) is a dioecious plant that emits 1,2-dimethoxybenzene (veratrole), a potent pollinator attractant to the nocturnal moth Hadena bicruris. Little is known about veratrole biosynthesis, although methylation of 2-methoxyphenol (guaiacol), another volatile emitted from white campion flowers, has been proposed. Here, we explore the biosynthetic route to veratrole. Feeding white campion flowers with [13C9]l-phenylalanine increased guaiacol and veratrole emission, and a significant portion of these volatile molecules contained the stable isotope. When white campion flowers were treated with the phenylalanine ammonia lyase inhibitor 2-aminoindan-2-phosphonic acid, guaiacol and veratrole levels were reduced by 50% and 63%, respectively. Feeding with benzoic acid (BA) or salicylic acid (SA) increased veratrole emission 2-fold, while [2H5]BA and [2H6]SA feeding indicated that the benzene ring of both guaiacol and veratrole is derived from BA via SA. We further report guaiacol O-methyltransferase (GOMT) activity in the flowers of white campion. The enzyme was purified to apparent homogeneity, and the peptide sequence matched that encoded by a recently identified complementary DNA (SlGOMT1) from a white campion flower expressed sequence tag database. Screening of a small population of North American white campion plants for floral volatile emission revealed that not all plants emitted veratrole or possessed GOMT activity, and SlGOMT1 expression was only observed in veratrole emitters. Collectively these data suggest that veratrole is derived by the methylation of guaiacol, which itself originates from phenylalanine via BA and SA, and therefore implies a novel branch point of the general phenylpropanoid pathway.
Subordinate removal affects parental investment, but not offspring survival in a cooperative cichlid
Authors: Bruintjes Rick , Heg‐Bachar Zina , Heg Dik
Published: April 2013

Subordinates in cooperative breeding systems may provide help to dominant pairs, who can benefit by either an increased total investment in their current brood or a reduced personal contribution to this investment. In the social cichlid Julidochromis ornatus, one large male subordinate generally spends 90% of his time in close proximity to the breeding shelter, whereas the dominants only spend 50% of their time close to the shelter.

We experimentally removed the large subordinate for 30 days (approximating one breeding cycle) to study the investment strategies of dominants and the effects on offspring survival, while accounting for subordinate immigration. Experimental groups were compared with control groups, from which subordinates were also caught but not removed. On day one following removal, we tested whether dominants overcompensated, fully compensated or undercompensated for absence of the subordinate on several parental behaviours. Moreover, we tested whether the pairs' potential compensatory behaviour remained high seven days following large subordinate removal.

One day following removal, dominants increased their time spent in the territory and their frequency of breeding shelter visits and defence, compared with the pre‐removal phase and control groups. The dominant pair overcompensated for the loss of subordinate help in their breeding shelter visits, fully compensated in defence and undercompensated their time spent in the territory. Seven days after large subordinate removal, behavioural differences between treatments had disappeared. However, when distinguishing between groups with or without a new immigrant subordinate, dominant pairs only diminished investment in the presence of an immigrant, suggesting a compensatory role of the large subordinate. Finally, survival of juvenile group members was not affected by the treatment.

Our experiments indicate that the presence of a large subordinate does not increase the dominant pairs' current reproductive success, but instead allows them to reduce their personal contribution to investment in the current brood. In addition, we illustrate that dominants may show strikingly different compensatory responses depending on the type of behaviour and emphasize the importance of immigrant subordinates to relieve dominants from costly compensatory responses in cooperative breeding systems.