bluuebunny/crossref_metadata_2025 huggingface dataset:
Overview on Spectral Line Source Finding and Visualisation
Authors: Koribalski B. S.
Published: August 2012

Here I will outline successes and challenges for finding spectral line sources in large data cubes that are dominated by noise. This is a 3D challenge as the sources we wish to catalog are spread over several spatial pixels and spectral channels. While 2D searches can be applied, e.g. channel by channel, optimal searches take into account the 3-dimensional nature of the sources. In this overview I will focus on Hi 21-cm spectral line source detection in extragalactic surveys, in particular HIPASS, the Hi Parkes All-Sky Survey and WALLABY, the ASKAP Hi All-Sky Survey. I use the original HIPASS data to highlight the diversity of spectral signatures of galaxies and gaseous clouds, both in emission and absorption. Among others, I report the discovery of a 680 km s−1 wide Hi absorption trough in the megamaser galaxy NGC 5793. Issues such as source confusion and baseline ripples, typically encountered in single-dish Hi surveys, are much reduced in interferometric Hi surveys. Several large Hi emission and absorption surveys are planned for the Australian Square Kilometre Array Pathfinder (ASKAP): here we focus on WALLABY, the 21-cm survey of the sky (δ < + 30°; z < 0.26) which will take about one year of observing time with ASKAP. Novel phased array feeds (‘radio cameras’) will provide 30 deg2 instantaneous field-of-view. WALLABY is expected to detect more than 500 000 galaxies, unveil their large-scale structures and cosmological parameters, detect their extended, low-surface-brightness disks as well as gas streams and filaments between galaxies. It is a precursor for future Hi surveys with SKA Phase I and II, exploring galaxy formation and evolution. The compilation of highly reliable and complete source catalogs will require sophisticated source-finding algorithms as well as accurate source parametrisation.
Data management pipeline for plant phenotyping in a multisite project
Authors: Billiau Kenny , Sprenger Heike , Schudoma Christian , Walther Dirk , Köhl Karin I.
Published: August 2012

In plant breeding, plants have to be characterised precisely, consistently and rapidly by different people at several field sites within defined time spans. For a meaningful data evaluation and statistical analysis, standardised data storage is required. Data access must be provided on a long-term basis and be independent of organisational barriers without endangering data integrity or intellectual property rights. We discuss the associated technical challenges and demonstrate adequate solutions exemplified in a data management pipeline for a project to identify markers for drought tolerance in potato. This project involves 11 groups from academia and breeding companies, 11 sites and four analytical platforms. Our data warehouse concept combines central data storage in databases and a file server and integrates existing and specialised database solutions for particular data types with new, project-specific databases. The strict use of controlled vocabularies and the application of web-access technologies proved vital to the successful data exchange between diverse institutes and data management concepts and infrastructures. By presenting our data management system and making the software available, we aim to support related phenotyping projects.
Characteristics of high-quality Asian elephant (Elephas maximus) ejaculates and in vitro sperm quality after prolonged chilled storage and directional freezing
Authors: O'Brien J. K. , Steinman K. J. , Montano G. A. , Love C. C. , Saiers R. L. , Robeck T. R.
Published: August 2012

The in vitro quality of spermatozoa from one elephant (Elephas maximus) was examined after chilled storage and directional freezing (DF). High-quality, non-contaminated ejaculates (77.6 ± 6.0% progressive motility, 3.9 ± 1.5 µg creatinine mL–1 raw semen, 2.7 ± 0.6% detached heads) were cryopreserved after 0 (0hStor), 12 (12hStor) and 24 h (24hStor) of chilled storage. At 0 h and 6 h post-thawing, total motility, plasma membrane integrity, acrosome integrity, mitochondrial activity and normal morphology were similar (P > 0.05) across treatments. In contrast, progressive motility, rapid velocity and several kinematic parameters were lower (P < 0.05) for 24Stor compared with 0hStor at 0 h post-thaw. By 6 h post-thaw, amplitude of lateral head displacement and velocity parameters (average pathway, straight-line and curvilinear velocity) were lower (P < 0.05) for 24hStor compared with 0hStor and 12hStor. DNA integrity was high and remained unchanged (P > 0.05) across all groups and processing stages (1.6 ± 0.6% of cells contained fragmented DNA). Results indicate that DF after up to 12 h of chilled storage results in a post-thaw sperm population of acceptable quality for artificial insemination. These findings have implications for the cryopreservation of sex-sorted spermatozoa, which typically undergo more than 12 h of chilled storage prior to sorting and preservation.
Characterising the chemistry of micropores in a sodic soil with strong texture-contrast using synchrotron X-ray techniques and LA-ICP-MS
Authors: Jassogne Laurence , Hettiarachchi Ganga , McNeill Ann , Chittleborough David
Published: August 2012

Soils with strong texture-contrast between A and B horizons dominate the agricultural zones of the west and south of Australia. The B horizon is often sodic and of much finer texture than the A (or E) horizon above, and can have a bulk density as high as 2 g cm–3. When dry, these B horizons may severely impede the root growth of annual cereal crops. The objective of this study was to characterise the mineralogy and chemistry of fine pores at the interface of an E and a sodic B horizon of an Alfisol (Sodosol). Micro-X-ray fluorescence spectroscopy (μ-XRF) was used to locate the distribution of calcium (Ca), manganese (Mn), iron (Fe), zinc (Zn), and copper (Cu), and μ-X-ray absorption near edge structure (μ-XANES) spectroscopy or μ-X-ray absorption fine structure (μ-XAFS) spectroscopy to investigate speciation of Fe, Mn, Zn, and Cu around a pore. Both natural aggregates and thin sections were employed but measurements from thin sections were more useful because of the smaller thickness of the sample. The distribution maps showed that Ca was present in the pores but the other elements were not. Copper, Mn, and Zn were concentrated around the micropore. Manganese was always well correlated with Fe.
Manganese was found in reduced form, i.e. Mn(II), and associated with phosphates, whereas Fe was in oxidised form and mostly associated with oxides. Zinc was mostly associated with carbonates (CO3), sulfates (SO4), and silicates (SiO4). The results were then compared with measurements by laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS). Only some of the observations made by μ-XRF were confirmed by LA-ICP-MS, most probably because of the superior detection limits of synchrotron-based μ-XRF.
Short-term effects of organic waste amendments on soil biota: responses of soil food web under eggplant cultivation
Authors: Eo Jinu , Park Kee-Choon , Park Byung-Bae
Published: August 2012

The aim of this study was to investigate the effects of reusable organic wastes on soil organisms, with a focus on changes in the soil food web. Bone meal, de-oiled cake, and oyster shell were applied at 5 t ha–1, and the abundance and biomass of soil organisms were measured at 4, 8, and 13 weeks after treatment in soil under eggplant cultivation. The abundance of microflora and fauna was higher in the soils treated with bone meal or de-oiled cake than in untreated soils, suggesting that soil organisms are affected by the quality of applied organic wastes. Increases in the abundance of bacterivorous nematodes were observed under treatment with bone meal or de-oiled cake, but there was little change in the abundance of predatory nematodes. A positive response of microarthropods in the Collembola and Oribatida was apparent, and these organisms are involved as secondary consumers in the soil food web, but the predaceous Gamasida were relatively unaffected. The abundance of protozoa, microbivorous nematodes, Collembola, and Oribatida was correlated with the abundance of bacteria and fungi, indicating that both bacteria- and fungi-based food webs formed. The abundance of the secondary consumers was not significantly correlated with that of the predators. The study suggested that, in the short-term, organic waste alters the primary and secondary consumers but its effect may not extend to predators.
Evaluation and modelling of furrow infiltration for uncropped ridge - furrow tillage in Loess Plateau soils
Authors: Zhang Yongyong , Wu Pute , Zhao Xining , Li Ping
Published: August 2012

The soil water dynamic process is critical for the design, management, and evaluation of ridge–furrow tillage in the semi-arid region of the Loess Plateau. The aim of this study was to determine the effectual infiltration variables, to evaluate the performance of four classical infiltration models, and to investigate the effect of those variables on the infiltration characteristics in a ridge–furrow configuration. Sixteen experimental treatments with two replications were conducted to monitor furrow infiltration in four types of Loess Plateau soils. The path analysis method was applied to quantify the effects of variables—opportunity time (T), initial soil water content (Q), bulk density (P), flow section area (S), and wetted perimeter (Wp) as independent variables—on cumulative infiltration (I). The results revealed that the direct effects of variables Wp, P, T, Q, and S on I were 0.751, –0.649, 0.291, –0.251, and –0.123, respectively. Variables Wp and P were the effectual components of furrow infiltration. The direct effect and total effect of Q on I were relatively minor compared with the other variables. The performance of four infiltration models (Philip model, Kostiakov–Lewis model, Kostiakov model, and Horton model) was investigated on the basis of evaluation indices. The Kostiakov–Lewis infiltration model with three parameters provided the best description of the relationship between cumulative infiltration and time. The influence of Wp on the constant coefficient k of the Kostiakov–Lewis model was significant. A furrow infiltration model taking Wp into consideration was developed. Validations in different Wp of two other soil types indicated that the soil water infiltration characteristics could be effectively simulated by the effectual variable based model for an uncropped ridge–furrow system. The information obtained from this research is useful in designing irrigation schemes and field management for ridge–furrow tillage.
Shift in C and N humification during legume litter decomposition in an acid tropical Ferralsol
Authors: Sierra Jorge , Motisi Natacha
Published: August 2012

Several long-term studies on tropical soils have shown that legume residue incorporation increases soil nitrogen (N) sequestration more than that of carbon (C), resulting in a fall in the C/N ratio. This study was designed to assess the short-term effect of legume litter addition on N supply and the long-term effect on soil organic matter (SOM) formation and soil C/N decrease. The long-term effect was evaluated in a 2-year mesocosm experiment with high and frequent organic inputs from two types of legume litter with different C/N ratios, using stable isotope techniques. The short-term effect of litter was analysed using four different litters in 3-month laboratory incubations. A model of litter decomposition was used to describe C and N kinetics in the laboratory experiment and to verify whether the long-term effect of litter may be predicted from short-term incubations. The results of the mesocosm experiment confirmed that legume inputs increased soil organic N (mean +21%) more than organic C (mean +15%) (P = 0.05). Although no differences between litters were observed for C dynamics, N sequestration (14% and 28%) and the final soil C/N (12.0 and 10.8) varied with litter C/N (34.4 and 16.1, respectively). The laboratory experiment and model outputs confirmed these findings and indicated that the higher N sequestration was due to a change in the parameters describing humification of C and N coming from litter. This change depended on litter quality and was greater for litters with low C/N—C humification 0.66 g C g–1 C and N humification 0.76 g N g–1 N for litter C/N 16.1. Carbon and N sequestration were greater in the laboratory experiment, due to a higher mineralisation of the new SOM derived from litter in the mesocosm experiment—32% and 15% for the mesocosm and the laboratory experiments, respectively. Our results indicated that the decrease in soil C/N and the rapid mineralisation of new SOM should be considered in models of litter decomposition to respond correctly to the long- and the short-term effects of legume litter inputs in tropical soils.
Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins
Authors: Eriksson Anders , Manica Andrea
Published: August 2012

Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.
Endothelial Semaphorin 7A promotes neutrophil migration during hypoxia
Authors: Morote-Garcia Julio César , Napiwotzky Daniel , Köhler David , Rosenberger Peter
Published: August 2012

Recent studies identified basic biological principles that are shared by the immune and the nervous system. One of these analogies applies to the orchestration of cellular migration where guidance proteins that serve as a stop signal for axonal migration can also serve as a stop signal for the migration of immune-competent cells. The control of leukocyte migration is of key interest during conditions associated with inflammatory tissue changes such as tissue hypoxia or hypoxic inflammation. Semaphorins are members of these axon guidance molecules. Previously unknown, we report here the expression and induction of semaphorin 7A (SEMA7A) on endothelium through hypoxia-inducible factor 1α during hypoxia. This induction of SEMA7A translates into increased transmigration of polymorphonuclear neutrophil granulocytes across endothelial cells. Extension of these findings demonstrated an attenuated extravasation of polymorphonuclear neutrophil granulocytes in Sema7a-deficient mice from the vasculature during hypoxia. Studies using chimeric animals identified the expression of Sema7A on nonhematopoietic tissue to be the underlying cause of the observed results. Taken together, our findings demonstrate that neuronal guidance proteins do not only serve as a stop signal for leukocyte migration but also can propagate the extravasation of leukocytes from the vascular space. Future anti-inflammatory strategies might be based on this finding.
Long-term model predictive control of gene expression at the population and single-cell levels
Authors: Uhlendorf Jannis , Miermont Agnès , Delaveau Thierry , Charvin Gilles , Fages François , Bottani Samuel , Batt Gregory , Hersen Pascal
Published: August 2012

Gene expression plays a central role in the orchestration of cellular processes. The use of inducible promoters to change the expression level of a gene from its physiological level has significantly contributed to the understanding of the functioning of regulatory networks. However, from a quantitative point of view, their use is limited to short-term, population-scale studies to average out cell-to-cell variability and gene expression noise and limit the nonpredictable effects of internal feedback loops that may antagonize the inducer action. Here, we show that, by implementing an external feedback loop, one can tightly control the expression of a gene over many cell generations with quantitative accuracy. To reach this goal, we developed a platform for real-time, closed-loop control of gene expression in yeast that integrates microscopy for monitoring gene expression at the cell level, microfluidics to manipulate the cells’ environment, and original software for automated imaging, quantification, and model predictive control. By using an endogenous osmostress responsive promoter and playing with the osmolarity of the cells environment, we show that long-term control can, indeed, be achieved for both time-constant and time-varying target profiles at the population and even the single-cell levels. Importantly, we provide evidence that real-time control can dynamically limit the effects of gene expression stochasticity. We anticipate that our method will be useful to quantitatively probe the dynamic properties of cellular processes and drive complex, synthetically engineered networks.
4-
O
-methylation of glucuronic acid in
Arabidopsis
glucuronoxylan is catalyzed by a domain of unknown function family 579 protein
Authors: Urbanowicz Breeanna R. , Peña Maria J. , Ratnaparkhe Supriya , Avci Utku , Backe Jason , Steet Heather F. , Foston Marcus , Li Hongjia , O’Neill Malcolm A. , Ragauskas Arthur J. , Darvill Alan G. , Wyman Charles , Gilbert Harry J. , York William S.
Published: August 2012

The hemicellulose 4-
O
-methyl glucuronoxylan is one of the principle components present in the secondary cell walls of eudicotyledonous plants. However, the biochemical mechanisms leading to the formation of this polysaccharide and the effects of modulating its structure on the physical properties of the cell wall are poorly understood. We have identified and functionally characterized an
Arabidopsis
glucuronoxylan methyltransferase (GXMT) that catalyzes 4-
O
-methylation of the glucuronic acid substituents of this polysaccharide. AtGXMT1, which was previously classified as a domain of unknown function (DUF) 579 protein, specifically transfers the methyl group from S-adenosyl-
l
-methionine to
O
-4 of α-
d
-glucopyranosyluronic acid residues that are linked to
O
-2 of the xylan backbone. Biochemical characterization of the recombinant enzyme indicates that GXMT1 is localized in the Golgi apparatus and requires Co
2+
for optimal activity in vitro. Plants lacking GXMT1 synthesize glucuronoxylan in which the degree of 4-
O
-methylation is reduced by 75%. This result is correlated to a change in lignin monomer composition and an increase in glucuronoxylan release during hydrothermal treatment of secondary cell walls. We propose that the DUF579 proteins constitute a previously undescribed family of cation-dependent, polysaccharide-specific
O
-methyl-transferases. This knowledge provides new opportunities to selectively manipulate polysaccharide
O
-methylation and extends the portfolio of structural targets that can be modified either alone or in combination to modulate biopolymer interactions in the plant cell wall.
Dimensional study of the caging order parameter at the glass transition
Authors: Charbonneau Patrick , Ikeda Atsushi , Parisi Giorgio , Zamponi Francesco
Published: August 2012

The glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed upon regarding why a fluid becomes sluggish while exhibiting but unremarkable structural changes. It is clear, however, that the process involves self-caging, which provides an order parameter for the transition. It is also broadly assumed that this cage should have a Gaussian shape in the mean-field limit. Here we show that this ansatz does not hold. By performing simulations as a function of spatial dimension
d
, we find the cage to keep a nontrivial form. Quantitative mean-field descriptions of the glass transition, such as mode-coupling theory, density functional theory, and replica theory, all miss this crucial element. Although the mean-field random first-order transition scenario of the glass transition is qualitatively supported here and non-mean-field corrections are found to remain small on decreasing
d
, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.
Infected CD8α
−
dendritic cells are the predominant source of IL-10 during establishment of persistent viral infection
Authors: Ng Cherie T. , Oldstone Michael B. A.
Published: August 2012

Interleukin-10 (IL-10) is an important factor involved in T-cell dysfunction during persistent viral infection. Although several factors can negatively regulate T-cell activity, targeting of the IL-10 pathway alone is sufficient to regenerate T-cell activity and increase viral control. How IL-10 mediates these effects is unclear. Here, we investigated the cellular source of IL-10 necessary for establishing T-cell exhaustion and viral persistence, using IL-10 reporter mice (VertX), cell-type–specific IL-10 and IL-10 receptor deletion mice, and bone marrow chimeric mice. During establishment of viral persistence, the cellular subset with the most prevalent expression of IL-10 was CD8α
−
CD4
+
dendritic cells (DCs), which produced IL-10 with increasing kinetics until 9 d postinfection. After this time point, DCs exhibited a modest decline in percentage of IL-10
+
cells whereas B cells and CD4
+
T cells increased minimally. Further analysis of the DC population demonstrated that IL-10 was primarily expressed in infected DCs. These DCs were a notable source of IL-10 as mutant mice with a DC-specific deletion of IL-10 had significantly decreased serum levels. Interestingly, viral infection was not directly causative of IL-10 expression; rather, IL-10 production appeared to be linked to type I IFN signaling. Our findings further illuminate the contribution of DCs to the production of IL-10 and to viral persistence.
A cellular model of memory reconsolidation involves reactivation-induced destabilization and restabilization at the sensorimotor synapse in
Aplysia
Authors: Lee Sue-Hyun , Kwak Chuljung , Shim Jaehoon , Kim Jung-Eun , Choi Sun-Lim , Kim Hyoung F. , Jang Deok-Jin , Lee Jin-A , Lee Kyungmin , Lee Chi-Hoon , Lee Young-Don , Miniaci Maria Concetta , Bailey Craig H. , Kandel Eric R. , Kaang Bong-Kiun
Published: August 2012

The memory reconsolidation hypothesis suggests that a memory trace becomes labile after retrieval and needs to be reconsolidated before it can be stabilized. However, it is unclear from earlier studies whether the same synapses involved in encoding the memory trace are those that are destabilized and restabilized after the synaptic reactivation that accompanies memory retrieval, or whether new and different synapses are recruited. To address this issue, we studied a simple nonassociative form of memory, long-term sensitization of the gill- and siphon-withdrawal reflex in
Aplysia
, and its cellular analog, long-term facilitation at the sensory-to-motor neuron synapse. We found that after memory retrieval, behavioral long-term sensitization in
Aplysia
becomes labile via ubiquitin/proteasome-dependent protein degradation and is reconsolidated by means of de novo protein synthesis. In parallel, we found that on the cellular level, long-term facilitation at the sensory-to-motor neuron synapse that mediates long-term sensitization is also destabilized by protein degradation and is restabilized by protein synthesis after synaptic reactivation, a procedure that parallels memory retrieval or retraining evident on the behavioral level. These results provide direct evidence that the same synapses that store the long-term memory trace encoded by changes in the strength of synaptic connections critical for sensitization are disrupted and reconstructed after signal retrieval.
The space-like surfaces with vanishing conformal form in the conformal space
Authors: Nie Changxiong
Published: August 2012

The conformal geometry of surfaces in the conformal spaceQ1n\mathbf {Q}^n_1is studied. We classify the space-like surfaces inQ1n\mathbf {Q}^n_1with vanishing conformal form up to conformal equivalence.
Influence of background treatment with mineralocorticoid receptor antagonists on ivabradine's effects in patients with chronic heart failure
Authors: Komajda Michel , Böhm Michael , Borer Jeffrey , Ford Ian , Krum Henry , Tase Adrian , Tavazzi Luigi , Swedberg Karl
Published: August 2012

Aims

A post‐hoc analysis of the SHIFT trial was performed to explore whether ivabradine is beneficial in patients with systolic heart failure, in sinus rhythm, with resting heart rate ≥70 b.p.m., and whose guideline‐recommended background therapy includes a mineralocorticoid receptor antagonist (MRA).

Methods and results

The effect of ivabradine on the primary composite endpoint of cardiovascular death or hospitalization for worsening heart failure, and its components, was explored in 3922 SHIFT patients with MRAs at baseline vs. 2583 patients without. Patients with MRAs were younger and were more likely to have severe heart failure and less coronary artery disease or hypertension than those without these drugs. Event rates in the placebo group were higher in patients with MRAs (33%) than in those without (23%) for the primary composite endpoint, with a 40% increase in relative risk (hazard ratio 1.40, 95% confidence interval 1.22–1.61). This was also true for secondary endpoints related to mortality or hospitalization. The effect of ivabradine on reducing the primary endpoint was similar in patients with and without MRAs (P = 0.916 for interaction, adjusted for prognostic factors at baseline), as were its effects on cardiovascular death (P = 0.279), hospitalizations for heart failure (P = 0.304), and death from heart failure and from all causes (P = 0.723 and 0.366, respectively). There was no difference in the safety of ivabradine in the two subpopulations.

Conclusion

Ivabradine improves outcomes in heart failure patients with heart rate ≥70 b.p.m. receiving multiple neurohormonal modulation treatments (angiotensin‐converting enzyme inhibitor or angiotensin receptor blocker, beta‐blocker, and MRA). The addition of ivabradine to multiple neurohormonal modulation should therefore be considered when the heart rate is ≥70 b.p.m.
Tibetan Hull‐less Barley (Hordeum vulgare L.) as a Potential Source of Antioxidants
Authors: Gong Ling‐Xiao , Jin Cheng , Wu Li‐Jiang , Wu Xiao‐Qin , Zhang Ying
Published: August 2012

Tibetan hull‐less barley grows at above 4,000 m altitude. One variety grown in the plain and three varieties grown in Tibet were collected from Tianjin and Lhasa. The barleys were polished into five fractions. Total soluble phenolic content (TSPC), total antioxidant capacity (TAC), and their correlation were investigated. Phenolic compounds were analyzed by HPLC, and TSPC content was evaluated by the Folin–Ciocalteu colorimetric method. TAC was measured using 2,2‐diphenyl‐1‐picrylhydrazyl, 2,2′‐azinobis‐(3‐ethylbenzthiazoline‐6‐sulfonate), and ferric reducing ability of plasma assays. Results showed that TSPC decreased from the outer to the inner fractions, with the outermost layer containing the highest (around 2,803–7,703 μg/g) and inner endosperm the lowest (around 870–1,348 μg/g). TSPC and TAC were highly and positively correlated (r = 0.9583–0.9710). Colored hull‐less barley had higher antioxidant activity than uncolored. TSPC and TAC of Tibetan varieties in the outer layers were more than two‐fold higher than that of Tianjin hull‐less barley. Tibetan hull‐less barley bran extracts are valuable sources of bioactive components with antioxidant activity.
A Multiplexed Immunofluorescence Method Identifies Phakopsora pachyrhizi Urediniospores and Determines Their Viability
Authors: Vittal R. , Haudenshield J. S. , Hartman G. L.
Published: August 2012

Soybean rust, caused by Phakopsora pachyrhizi, occurs concomitantly wherever soybean is grown in the tropical and subtropical regions of the world. After reports of its first occurrence in Brazil in 2001 and the continental United States in 2004, research on the disease and its pathogen has greatly increased. One area of research has focused on capturing urediniospores, primarily by rain collection or wind traps, and detecting them either by microscopic observations or by immunological or molecular techniques. This system of detection has been touted for use as a potential warning system to recommend early applications of fungicides. One shortcoming of the method has been an inability to determine whether the spores are viable. Our study developed a method to detect viable P. pachyrhizi urediniospores using an immunofluorescence assay combined with propidium iodide (PI) staining. Antibodies reacted to P. pachyrhizi and other Phakopsora spp. but did not react with other common soybean pathogens or most other rust fungi tested, based on an indirect immunofluorescence assay using fluorescein isothiocyanate-labeled secondary antibodies. Two vital staining techniques were used to assess viability of P. pachyrhizi urediniospores: one combined carboxy fluorescein diacetate (CFDA) and PI, and the other utilized (2-chloro-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenylquinolinium iodide] (FUN 1). Using the CFDA-PI method, viable spores stained green with CFDA and nonviable spores counterstained red with PI. Using the FUN 1 method, cylindrical intravacuolar structures were induced to form within metabolically active urediniospores, causing them to fluoresce bright red to reddish-orange, whereas dead spores, with no metabolic activity, had an extremely diffused, faint fluorescence. An immunofluorescence technique in combination with PI counterstaining was developed to specifically detect viable P. pachyrhizi urediniospores. The method is rapid and reliable, with a potential for application in forecasting soybean rust based on the detection of viable urediniospores.
Genetic background affects epistatic interactions between two beneficial mutations
Authors: Wang Yinhua , Díaz Arenas Carolina , Stoebel Daniel M. , Cooper Tim F.
Published: August 2012

The phenotypic effect of mutations can depend on their genetic background, a phenomenon known as epistasis. Many experimental studies have found that epistasis is pervasive, and some indicate that it may follow a general pattern dependent on the fitness effect of the interacting mutations. These studies have, however, typically examined the effect of interactions between a small number of focal mutations in a single genetic background. Here, we extend this approach by considering how the interaction between two beneficial mutations that were isolated from a population of laboratory evolvedEscherichia colichanges when they are added to divergent natural isolate strains ofE. coli. We find that interactions between the focal mutations and the different genetic backgrounds are common. Moreover, the pair-wise interaction between the focal mutations also depended on their genetic background, being more negative in backgrounds with higher absolute fitness. Together, our results indicate the presence of interactions between focal mutations, but also caution that these interactions depend quantitatively on the wider genetic background.
Recent advances in mapping environmental microbial metabolisms through13C isotopic fingerprints
Authors: Tang Joseph Kuo-Hsiang , You Le , Blankenship Robert E. , Tang Yinjie J.
Published: August 2012

After feeding microbes with a defined13C substrate, unique isotopic patterns (isotopic fingerprints) can be formed in their metabolic products. Such labelling information not only can provide novel insights into functional pathways but also can determine absolute carbon fluxes through the metabolic network via metabolic modelling approaches. This technique has been used for finding pathways that may have been mis-annotated in the past, elucidating new enzyme functions, and investigating cell metabolisms in microbial communities. In this review paper, we summarize the applications of13C approaches to analyse novel cell metabolisms for the past 3 years. The isotopic fingerprints (defined as unique isotopomers useful for pathway identifications) have revealed the operations of the Entner–Doudoroff pathway, the reverse tricarboxylic acid cycle, new enzymes for biosynthesis of central metabolites, diverse respiration routes in phototrophic metabolism, co-metabolism of carbon nutrients and novel CO2fixation pathways. This review also discusses new isotopic methods to map carbon fluxes in global metabolisms, as well as potential factors influencing the metabolic flux quantification (e.g. metabolite channelling, the isotopic purity of13C substrates and the isotopic effect). Although13C labelling is not applicable to all biological systems (e.g. microbial communities), recent studies have shown that this method has a significant value in functional characterization of poorly understood micro-organisms, including species relevant for biotechnology and human health.
Characterizing and optimizing poly-
l
-lactide-co-ε-caprolactone membranes for urothelial tissue engineering
Authors: Sartoneva Reetta , Haaparanta Anne-Marie , Lahdes-Vasama Tuija , Mannerström Bettina , Kellomäki Minna , Salomäki Minna , Sándor George , Seppänen Riitta , Miettinen Susanna , Haimi Suvi
Published: August 2012

Different synthetic biomaterials such as polylactide (PLA), polycaprolactone and poly-
l
-lactide-co-ε-caprolactone (PLCL) have been studied for urothelial tissue engineering, with favourable results. The aim of this research was to further optimize the growth surface for human urothelial cells (hUCs) by comparing different PLCL-based membranes: smooth (s) and textured (t) PLCL and knitted PLA mesh with compression-moulded PLCL (cPLCL). The effects of topographical texturing on urothelial cell response and mechanical properties under hydrolysis were studied. The main finding was that both sPLCL and tPLCL supported hUC growth significantly better than cPLCL. Interestingly, tPLCL gave no significant advantage to hUC attachment or proliferation compared with sPLCL. However, during the 14 day assessment period, the majority of cells were viable and maintained phenotype on all the membranes studied. The material characterization exhibited potential mechanical characteristics of sPLCL and tPLCL for urothelial applications. Furthermore, the highest elongation of tPLCL supports the use of this kind of texturing. In conclusion, in light of our cell culture results and mechanical characterization, both sPLCL and tPLCL should be further studied for urothelial tissue engineering.
The role of capture spiral silk properties in the diversification of orb webs
Authors: Tarakanova Anna , Buehler Markus J.
Published: August 2012

Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification.
Epidermis architecture and material properties of the skin of four snake species
Authors: Klein Marie-Christin G. , Gorb Stanislav N.
Published: August 2012

On the basis of structural and experimental data, it was previously demonstrated that the snake integument consists of a hard, robust, inflexible outer surface (Oberhäutchenand β-layer) and softer, flexible inner layers (α-layers). It is not clear whether this phenomenon is a general adaptation of snakes to limbless locomotion or only to specific conditions, such as habitat and locomotion. The aim of the present study was to compare the structure and material properties of the outer scale layers (OSLs) and inner scale layers (ISLs) of the exuvium epidermis in four snake species specialized to live in different habitats:Lampropeltis getula californiae(terrestrial),Epicrates cenchria cenchria(generalist),Morelia viridis(arboreal) andGongylophis colubrinus(sand-burrowing). Scanning electron microscopy (SEM) of skin cross sections revealed a strong variation in the epidermis structure between species. The nanoindentation experiments clearly demonstrated a gradient of material properties along the epidermis in the integument of all the species studied. The presence of such a gradient is a possible adaptation to locomotion and wear minimization on natural substrates. In general, the difference in both the effective elastic modulus and hardness of the OSL and ISL between species was not large compared with the difference in epidermis thickness and architecture.
Costs of a more spacious home after remodelling by hermit crabs
Authors: Laidre Mark E. , Patten Eli , Pruitt Lisa
Published: August 2012

Architectural creations occur throughout the animal kingdom, with invertebrates and vertebrates building structures such as homes to maximize their Darwinian fitness. Animal architects face many trade-offs in building optimally designed structures. But what about animals that do not build, and those that only remodel the original creations of others: do such secondary architects face similar trade-offs? Recent evidence has revealed that hermit crabs—animals well known for opportunistically moving into remnant gastropod shells—can also act as secondary architects, remodelling the shells they inherit from gastropods. Remodelling has only been found among terrestrial hermits (Coenobitaspp.), not marine hermits. Here we investigate the potential trade-offsCoenobita compressusfaces from remodelling by subjecting its remodelled and unremodelled homes to controlled engineering crush tests, which parallel the homes being crushed by predators. While remodelled homes are significantly more spacious and lightweight than unremodelled homes, we find that the homes attain these beneficial qualities at a cost: a reduced resistance to being crushed. Hermit crabs may therefore only remodel their homes to thresholds set by the bite force of their predators. Our results suggest that, like primary animal architects, which face trade-offs when optimizing architectural designs, secondary animal architects face trade-offs when remodelling such designs.
Influences of surface chemistry and swelling of salt-treated polyelectrolyte multilayers on migration of smooth muscle cells
Authors: Han Lulu , Mao Zhengwei , Wu Jindan , Zhang Yuying , Gao Changyou
Published: August 2012

The cell migration plays a crucial role in a variety of physiological and pathological processes and can be regulated by the cell–substrate interactions. We found previously that the poly(sodium 4-styrenesulphonate) (PSS)/poly(diallyldimethylammonium) chloride (PDADMAC) multilayers post-treated in 1–5 M NaCl solutions result in continuous changes of their physico-chemical properties such as thickness, chemical composition, surface charge, swelling ratio and wettability. In this study, the responses of human smooth muscle cells (SMCs) on these salt-treated multilayers, particularly the governing factors of cellular migration that offer principles for designing therapeutics and implants, were disclosed. The cell migration rate was slowest on the 3 M NaCl-treated multilayers, which was comparable with that on tissue culture plates, but it was highest on 5 M NaCl-treated multilayers. To elucidate the intrinsic mechanisms, cell adhesion, proliferation, adhesion and related gene expressions were further investigated. The SMCs preferred to attach, spread and proliferate on the PSS-dominated surfaces with well-organized focal adhesion and actin fibres, especially on the 3 M NaCl-treated multilayers, while were kept round and showed low viability on the PDADMAC-dominated surfaces. The relative mRNA expression levels of adhesion-related genes such as fibronectin, laminin and focal adhesion kinase, and migration-related genes such as myosin IIA and Cdc42 were compared to explain the different cellular behaviours. These results reveal that the surface chemistry and the swelling of the salt-treated multilayers govern the cell migration behaviours.
Stresslet asymptotics for a treadmilling swimmer near a two-dimensional corner: hydrodynamic bound states
Authors: Davis Anthony M. J. , Crowdy Darren G.
Published: August 2012

The dynamics of a circular treadmilling low Reynolds number swimmer near a right-angled corner is studied in the asymptotic limit in which the radius of the treadmiller is small. The governing dynamical equations are found explicitly, correct to third order in the swimmer radius, by means of Mellin transform techniques. The existence of arc-like periodic orbits, or ‘hydrodynamic bound states’, in the corner region is identified, and these orbits are found to be attractors in the dynamics for a large range of initial swimmer locations and orientations. The analytical approach may be extended to wedge regions of other fractional angles.
Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge
Authors: Morelli Toni Lyn , Smith Adam B. , Kastely Christina R. , Mastroserio Ilaria , Moritz Craig , Beissinger Steven R.
Published: August 2012

We conducted detailed resurveys of a montane mammal,
Urocitellus beldingi
, to examine the effects of climate change on persistence along the trailing edge of its range. Of 74 California sites where
U. beldingi
were historically recorded (1902–1966), 42 per cent were extirpated, with no evidence for colonization of previously unoccupied sites. Increases in both precipitation and temperature predicted site extirpations, potentially owing to snowcover loss. Surprisingly, human land-use change buffered climate change impacts, leading to increased persistence and abundance. Excluding human-modified sites,
U. beldingi
has shown an upslope range retraction of 255 m. Generalized additive models of past distribution were predictive of modern range contractions (AUC = 0.76) and projected extreme reductions (52% and 99%, respectively) of
U. beldingi's
southwestern range to 2080 climates (Hadley and CCCMA A2). Our study suggests the strong impacts of climate change on montane species at their trailing edge and how anthropogenic refugia may mitigate these effects.
Neural control of tuneable skin iridescence in squid
Authors: Wardill T. J. , Gonzalez-Bellido P. T. , Crook R. J. , Hanlon R. T.
Published: August 2012

Fast dynamic control of skin coloration is rare in the animal kingdom, whether it be pigmentary or structural. Iridescent structural coloration results when nanoscale structures disrupt incident light and selectively reflect specific colours. Unlike animals with fixed iridescent coloration (e.g. butterflies), squid iridophores (i.e. aggregations of iridescent cells in the skin) produce
dynamically tuneable structural coloration
, as exogenous application of acetylcholine (ACh) changes the colour and brightness output. Previous efforts to stimulate iridophores neurally or to identify the source of endogenous ACh were unsuccessful, leaving researchers to question the activation mechanism. We developed a novel neurophysiological preparation in the squid
Doryteuthis pealeii
and demonstrated that electrical stimulation of neurons in the skin shifts the spectral peak of the reflected light to shorter wavelengths (greater than 145 nm) and increases the peak reflectance (greater than 245%) of innervated iridophores. We show ACh is released within the iridophore layer and that extensive nerve branching is seen within the iridophore. The dynamic colour shift is significantly faster (17 s) than the peak reflectance increase (32 s), revealing two distinct mechanisms. Responses from a structurally altered preparation indicate that the reflectin protein condensation mechanism explains peak reflectance change, while an undiscovered mechanism causes the fast colour shift.
Diversification rates and the latitudinal gradient of diversity in mammals
Authors: Soria-Carrasco Víctor , Castresana Jose
Published: August 2012

The latitudinal gradient of species richness has frequently been attributed to higher diversification rates of tropical groups. In order to test this hypothesis for mammals, we used a set of 232 genera taken from a mammalian supertree and, additionally, we reconstructed dated Bayesian phylogenetic trees of 100 genera. For each genus, diversification rate was estimated taking incomplete species sampling into account and latitude was assigned considering the heterogeneity in species distribution ranges. For both datasets, we found that the average diversification rate was similar among all latitudinal bands. Furthermore, when we used phylogenetically independent contrasts, we did not find any significant correlation between latitude and diversification parameters, including different estimates of speciation and extinction rates. Thus, other factors, such as the dynamics of dispersal through time, may be required to explain the latitudinal gradient of diversity in mammals.
Epistasis from functional dependence of fitness on underlying traits
Authors: Chiu Hsuan-Chao , Marx Christopher J. , Segrè Daniel
Published: August 2012

Epistasis between mutations in two genes is thought to reflect an interdependence of their functions. While sometimes epistasis is predictable using mechanistic models, its roots seem, in general, hidden in the complex architecture of biological networks. Here, we ask how epistasis can be quantified based on the mathematical dependence of a system-level trait (e.g. fitness) on lower-level traits (e.g. molecular or cellular properties). We first focus on a model in which fitness is the difference between a benefit and a cost trait, both pleiotropically affected by mutations. We show that despite its simplicity, this model can be used to analytically predict certain properties of the ensuing distribution of epistasis, such as a global negative bias, resulting in antagonism between beneficial mutations, and synergism between deleterious ones. We next extend these ideas to derive a general expression for epistasis given an arbitrary functional dependence of fitness on other traits. This expression demonstrates how epistasis relative to fitness can emerge despite the absence of epistasis relative to lower level traits, leading to a formalization of the concept of independence between biological processes. Our results suggest that epistasis may be largely shaped by the pervasiveness of pleiotropic effects and modular organization in biological networks.