bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of intake of diets containing tannins and saponins on in vitro gas production and sheep performance
Authors: Barros-Rodríguez M. A. , Solorio-Sánchez F. J. , Sandoval-Castro C. A. , Ahmed A. M. M. , Rojas-Herrera R. , Briceño-Poot E. G. , Ku-Vera J. C.
Published: July 2014

The aim of this study was to evaluate the effect of the intake of leucaena, Enterolobium cyclocarpum, fruits and a mixture of both feeds on in vitro gas production and in vivo sheep productive performance. The experiment was conducted at the University of Yucatan, Mexico. Twenty-four Pelibuey sheep, 20.28 ± 2.99 kg average liveweight (LW), were used. Animals were randomly assigned to the following experimental treatments: T1: 100% Pennisetum purpureum, T2: 30% Leucaena leucocephala foliage + 70% P. purpureum, T3: 30% E. cyclocarpum fruits + 70% P. purpureum, T4: 30% L. leucocephala foliage + 30% E. cyclocarpum fruits + 40% P. purpureum. Voluntary intake was higher in T4 (grass + leucaena + E. cyclocarpum) (P = 0.0001). Higher LW gain was observed in animals fed with T4 (P = 0.0001) and the lowest LW gains were recorded with grass (T1) and grass + leucaena (T2) (78.9 and 99.2 g/day, respectively). Similarly, the feed conversion efficiency was improved with treatment T4 (P = 0.0030). The in vitro gas production (48 h) was lower by 30 mL/0.5 g fermented DM in T4 compared with the other treatments (P = 0.0001). Apparent DM digestibility was higher in T3 and T4 (P = 0.0005). The protozoa counts were lower in T2, T3 and T4 (P = 0.0001). Higher intake, digestibility and sheep performance with diets containing grass + leucaena + E. cyclocarpum mixture arise from an improved nutritional diet as these sources have higher protein, lower cell walls and higher DM digestibility.
Expanding the contribution of dairy goats in efficient and sustainable production systems
Authors: Liang J. B. , Devendra C.
Published: July 2014

Goats contribute significantly to human nutrition, food security and income of resource-poor small farmers in Asia, Africa and beyond. Because of the high content of mono- and polyunsaturated fatty acids in goat milk, it is beneficial for human health resulting in it being sold at premium prices of three to nine times the price of cow milk in countries like China, Malaysia, Indonesia and Thailand. Goats play a significant role in farming systems that directly impact on the capacity of rural farmers striving for the objective of sustainable food production systems. Increasing sustainable food production, particularly of animal proteins, presents major challenges to these small farms in the face of massive demands that are driven by rapid growth of human populations and increased availability of disposable income. In the last two decades, expanding market demand for goat milk has resulted in the establishment of commercial dairy goat farms in several newly developed South-east Asian countries. Major challenges to expanding production exist, and include ways to utilise the well-adapted features inherent in goats and their potential production to benefit the small and commercial farmers alike. Increasing the knowledge base is a priority to stimulate improved production systems and, increased the income of dairy goat farmers and other people involved in the industry. The recent establishment of the Asian-Australasian Dairy Goat Network supported jointly by FAO and Universiti Putra Malaysia, and national programs of participating countries, are committed to address these objectives and facilitate much-needed improvements to sustain dairy goat production systems in Asia and beyond.
Do wide crowns in arid woodland trees reflect hydraulic limitation and reduction of self-shading?
Authors: Escoto-Rodríguez Martín , Facelli José M. , Watling Jennifer R.
Published: July 2014

In arid regions many tree species develop broad crowns. A number of hypotheses involve trade-offs between growth in height and horizontal spreading, but there is no explanation for the switch from vertical to horizontal growth during development. Using Acacia papyrocarpa Benth as a model, we measured tree height and crown shape across different sites and topographic positions. We also measured δ13C of phyllodes from crown tops and lateral spreading branches. Trees were significantly taller at the base of a hill, where water availability is typically greater, than on the adjacent steep hillslope. In contrast, δ13C from the treetops was not significantly different across this topographic gradient, despite variation in tree height. In addition, δ13C was higher at treetops than in lower, lateral branches. These observations are consistent with hydraulic limitation to tree height. The shape of mature and young crowns in open environments was not symmetrical. At all sites, branches were shortest, but tree crowns tallest, on south-facing (i.e. shadiest) aspect of crowns. This suggests that light limitation may also affect crown development. If upper branches become water-limited and lower branches light-limited, then middle lateral branches become the less-stressed part of the crown and may grow more, producing a broad crown.
Food, food choice and nutrition promotion in a remote Australian Aboriginal community
Authors: Colles Susan L. , Maypilama Elaine , Brimblecombe Julie
Published: July 2014

Contemporary diets of Aboriginal people living in remote Australia are characterised by processed foods high in fat and sugar. Within the ‘new’ food system, evidence suggests many Aboriginal people understand food in their own terms but lack access to consumer information about store-purchased foods, and parents feel inadequate as role models. In a remote Australian Aboriginal community, purposive sampling identified adults who participated in semistructured interviews guided by food-based themes relating to the contemporary food system, parental guidance of children’s food choice and channels through which people learn. Interpretive content analysis was used to identify salient themes. In discussions, people identified more closely with dietary qualities or patterns than nutrients, and valued a balanced, fresh diet that made them feel ‘light’. People possessed basic knowledge of ‘good’ store foods, and wanted to increase familiarity and experience with foods in packets and cans through practical and social skills, especially cooking. Education about contemporary foods was obtained from key family role models and outside the home through community-based organisations, including school, rather than pamphlets and flip charts. Freedom of choice was a deeply held value; carers who challenged children’s autonomy used strategic distraction, or sought healthier alternatives that did not wholly deny the child. Culturally safe approaches to information sharing and capacity building that contribute to the health and wellbeing of communities requires collaboration and shared responsibility between policy makers, primary healthcare agencies, wider community-based organisations and families.
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
Authors: Hawley Alyse K. , Brewer Heather M. , Norbeck Angela D. , Paša-Tolić Ljiljana , Hallam Steven J.
Published: July 2014

Significance

Oxygen is an important organizing principle in marine ecosystems. As oxygen levels decline, energy is increasingly diverted away from higher trophic levels into microbial community metabolism causing changes in carbon and nutrient cycling. Here we use metagenomic and metaproteomic methods to chart in situ metabolic networks linking key microbial players driving carbon and nutrient cycling in a seasonally stratified fjord, Saanich Inlet, a model ecosystem for studying microbial responses to changing levels of water column oxygen deficiency. Based on this evidence, we develop a conceptual model that describes coupling of chemotrophic energy production with dark carbon fixation along defined redox gradients with implications for primary production and possibly carbon sedimentation in expanding marine oxygen minimum zones.
Intravital imaging of cardiac function at the single-cell level
Authors: Aguirre Aaron D. , Vinegoni Claudio , Sebas Matt , Weissleder Ralph
Published: July 2014

Significance

Despite advances in cardiac imaging technologies such as MRI, computed tomography, and ultrasound it has not been possible to image cardiac function in animal models at the cellular level owing to insufficient resolution and excess motion. As a result, our understanding of cardiac biology and function is derived from either whole-organ imaging techniques or from isolated in vitro heart preparations and cellular model systems. We demonstrate a technique for intravital optical microscopy that compensates for motion of the contracting heart and allows for measurement of contractile function at the single-cell level. These approaches will enable studies of complex and dynamic cellular physiology in the beating heart and should be widely useful for studying heart disease in animal models.
The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of
Arabidopsis
Authors: Rautengarten Carsten , Ebert Berit , Moreno Ignacio , Temple Henry , Herter Thomas , Link Bruce , Doñas-Cofré Daniela , Moreno Adrián , Saéz-Aguayo Susana , Blanco Francisca , Mortimer Jennifer C. , Schultink Alex , Reiter Wolf-Dieter , Dupree Paul , Pauly Markus , Heazlewood Joshua L. , Scheller Henrik V. , Orellana Ariel
Published: July 2014

Significance

Delivery of nucleotide sugar substrates into the Golgi apparatus and endoplasmic reticulum for processes such as cell wall biosynthesis and protein glycosylation is critical for plant growth and development. Plant genomes encode large families of uncharacterized nucleotide sugar transporters that are specifically presumed to deliver the diverse array of nucleotide sugars found in plants. This study has developed a novel approach that enabled functional characterization of six bifunctional UDP-rhamnose (Rha)/UDP-galactose (Gal) transporters from
Arabidopsis
. An analysis of loss-of-function and overexpression lines for two of these transporters identified biochemical alterations supporting their roles in the biosynthesis of Rha- and Gal-containing polysaccharides. Thus, cell wall polysaccharide biosynthesis in the Golgi apparatus of plants is likely also regulated by substrate transport mechanisms.
Helical motion of the cell body enhances
Caulobacter crescentus
motility
Authors: Liu Bin , Gulino Marco , Morse Michael , Tang Jay X. , Powers Thomas R. , Breuer Kenneth S.
Published: July 2014

Significance

Using a digital tracking microscope that provides both cell position and orientation, we have correlated the detailed motion of the cell body of a fast-swimming bacterium,
Caulobacter crescentus
, with its swimming motility. Contrary to the prevailing view that the rotating flagellum is the only means to propel the cell, we show that when the flagellum pushes the cell, the axis of the cell body precesses with a helical trajectory that enhances motility. This discovery changes our understanding regarding the role that cell shape and motion plays in bacterial motility. Furthermore, our powerful cell tracking technique enables a wide variety of studies that require extended observation of single cells, including motility, cell behavior, and aging.
Arsenite oxidation by a facultative chemolithoautotrophicSinorhizobiumsp. KGO-5 isolated from arsenic-contaminated soil
Authors: Dong Dan , Ohtsuka Toshihiko , Dong Dian Tao , Amachi Seigo
Published: July 2014

A chemolithoautotrophic arsenite-oxidizing bacterium, designated strain KGO-5, was isolated from arsenic-contaminated industrial soil. Strain KGO-5 was phylogenetically closely related with Sinorhizobium meliloti with 16S rRNA gene similarity of more than 99%, and oxidized 5 mM arsenite under autotrophic condition within 60 h with a doubling time of 3.0 h. Additions of 0.01–0.1% yeast extract enhanced the growth significantly, and the strain still oxidized arsenite efficiently with much lower doubling times of approximately 1.0 h. Arsenite-oxidizing capacities (11.2–54.1 μmol h−1 mg dry cells−1) as well as arsenite oxidase (Aio) activities (1.76–10.0 mU mg protein−1) were found in the cells grown with arsenite, but neither could be detected in the cells grown without arsenite. Strain KGO-5 possessed putative aioA gene, which is closely related with AioA of Ensifer adhaerens. These results suggest that strain KGO-5 is a facultative chemolithoautotrophic arsenite oxidizer, and its Aio is induced by arsenic.
Molecular cloning, expression profiles, and characterization of a novel polyphenol oxidase (PPO) gene in Hevea brasiliensis
Authors: Li Dejun , Deng Zhi , Liu Changren , Zhao Manman , Guo Huina , Xia Zhihui , Liu Hui
Published: July 2014

The polyphenol oxidase (PPO) is involved in undesirable browning in many plant foods. Although the PPOs have been studied by several researchers, the isolation and expression profiles of PPO gene were not reported in rubber tree. In this study, a new PPO gene, HbPPO, was isolated from Hevea brasiliensis. The sequence alignment showed that HbPPO indicated high identities to plant PPOs and belonged to dicot branch. The cis-acting regulatory elements related to stress/hormone responses were predicted in the promoter region of HbPPO. Real-time RT-PCR analyses showed that HbPPO expression varied widely depending on different tissues and developmental stages of leaves. Besides being associated with tapping panel dryness, the HbPPO transcripts were regulated by ethrel, wounding, H2O2, and methyl jasmonate treatments. Moreover, the correlation between latex coagulation rate and PPO activity was further confirmed in this study. Our results lay the foundation for further analyzing the function of HbPPO in rubber tree.
Enhanced protection of pathogenic Escherichia coli ingested by a soil nematode Caenorhabditis elegans against sanitizer treatments
Authors: Park Mi Ri , Oh Sangnam , Yun Hyun Sun , Kim Soon Han , Ko Young Ho , Ryu Jee-Hoon , Rhee Min Suk , Shin Ok Sarah , Kim Younghoon
Published: July 2014

We employed Caenorhabditis elegans as a model to study the effectiveness of sanitizers in killing pathogenic Escherichia coli strains ingested by free-living nematodes. Adult worms that had fed on six pathogenic E. coli strains (highly persistent in the nematode intestine) were treated with three chemical solutions. In planktonic cells, none of the H2O2 and acetic acid treatments influenced the survival of the pathogenic E. coli strains, whereas sodium hypochlorite critically decreased the viability of the strains. Importantly, the survival of the E. coli strains was dramatically increased by persistence in the C. elegans gut under 0.1% sodium hypochlorite, and several strains could survive at a concentration of 0.5%. In addition, all pathogenic E. coli strains in the C. elegans gut survived on the lettuce for 5 days even though they were washed with 0.1% sodium hypochlorite. Taken together, our results indicate that pathogenic E. coli ingested by C. elegans may be protected against washing treatment with commercial sanitizers on raw food materials.
Microtubule-associated protein (MAP) 4 interacts with microtubules in an intrinsically disordered manner
Authors: Hashi Yurika , Kawai Gota , Kotani Susumu
Published: July 2014

We previously used nuclear magnetic resonance (NMR) to analyze the structure of a synthetic tricosapeptide corresponding to an active site of microtubule-associated protein 4 (MAP4). To further the structural analysis, we have constructed a minimal active domain fragment of MAP4, encompassing the entire active site, and obtained its NMR spectra. The secondary structure prediction using partially assigned NMR data suggested that the fragment is largely unfolded. Two other independent techniques also demonstrated its unfolded nature, indicating that MAP4 belongs to the class of intrinsically disordered proteins (IDPs). The NMR spectra of the fragment-microtubule mixture revealed that the fragment binds to the microtubule using multiple binding sites, apparently contradicting our previous quantitative studies. Given that MAP4 is intrinsically disordered, we propose a mechanism in which any one of the binding sites is active at a time, which is one of the typical interaction mechanisms proposed for IDPs.
The Bourbon monarchy and prison legislation in Sicily: two competing plans for reform (1826–1830)
Authors: Fazio Simona
Published: July 2014

The nineteenth century was a critical phase in the construction of European penitentiary systems. The eighteenth century had seen the evolution of the concept of punishment and the corresponding development of the practice of imprisonment as central to new ideas about penal sanctions. As a result, between 1830 and 1848 grand plans to reform prison systems were put forward in almost all the larger European countries. The Kingdom of the Two Sicilies played its part in this process: an innovative reform plan was developed here, ahead of the rest of the Italian peninsula, which was fully implemented between 1832 and 1845 but had its origins in an earlier period, being given its initial impetus by modernisation on the legislative front. Sicily was particularly rich in terms of legal experimentation in this area. Here, informed by the most recent developments in contemporary science, plans to reform prison legislation were produced as early as the 1820s; these attest to the interest with which lawyers, philanthropists and government officials approached the issue. The analysis of two plans discovered in theArchivio di Statoin Palermo is especially helpful in demonstrating the existence of a ‘workshop for prison legislation’ that addressed concrete problems while also being the manifestation of a sophisticated legal culture.
Comparison of Prior Authorization and Prospective Audit with Feedback for Antimicrobial Stewardship
Authors: Mehta Jimish M. , Haynes Kevin , Wileyto E. Paul , Gerber Jeffrey S. , Timko Daniel R. , Morgan Steven C. , Binkley Shawn , Fishman Neil O. , Lautenbach Ebbing , Zaoutis Theoklis
Published: July 2014

(See the commentary by Van Schooneveld and Rupp, on pages1100–1102.)

Objective

Although prior authorization and prospective audit with feedback are both effective antimicrobial stewardship program (ASP) strategies, the relative impact of these approaches remains unclear. We compared these core ASP strategies at an academic medical center.

Design

Quasi-experimental study.

Methods

We compared antimicrobial use during the 24 months before and after implementation of an ASP strategy change. The ASP used prior authorization alone during the preintervention period, June 2007 through May 2009. In June 2009, many antimicrobials were unrestricted and prospective audit was implemented for cefepime, piperacillin/tazobactam, and vancomycin, marking the start of the postintervention period, July 2009 through June 2011. All adult inpatients who received more than or equal to 1 dose of an antimicrobial were included. The primary end point was antimicrobial consumption in days of therapy per 1,000 patient-days (DOT/1,000-PD). Secondary end points included length of stay (LOS).

Results

In total, 55,336 patients were included (29,660 preintervention and 25,676 postintervention). During the preintervention period, both total systemic antimicrobial use (−9.75 DOT/1,000-PD per month) and broad-spectrum anti-gram-negative antimicrobial use (−4.00 DOT/1,000-PD) declined. After the introduction of prospective audit with feedback, however, both total antimicrobial use (+9.65 DOT/1,000-PD per month; P < .001) and broad-spectrum anti-gram-negative antimicrobial use (+4.80 DOT/1,000-PD per month; P < .001) increased significantly. Use of cefepime and piperacillin/tazobactam both significantly increased after the intervention (P = .03). Hospital LOS and LOS after first antimicrobial dose also significantly increased after the intervention (P = .016 and .004, respectively).

Conclusions

Significant increases in antimicrobial consumption and LOS were observed after the change in ASP strategy.

Infect Control Hosp Epidemiol 2014;35(9):1092-1099
Multisite Exploration of Clinical Decision Making for Antibiotic Use by Emergency Medicine Providers Using Quantitative and Qualitative Methods
Authors: May Larissa , Gudger Glencora , Armstrong Paige , Brooks Gillian , Hinds Pamela , Bhat Rahul , Moran Gregory J. , Schwartz Lisa , Cosgrove Sara E. , Klein Eili Y. , Rothman Richard E. , Rand Cynthia
Published: July 2014

Objectives.

To explore current practices and decision making regarding antimicrobial prescribing among emergency department (ED) clinical providers.

Methods

We conducted a survey of ED providers recruited from 8 sites in 3 cities. Using purposeful sampling, we then recruited 21 providers for in-depth interviews. Additionally, we observed 10 patient-provider interactions at one of the ED sites. SAS 9.3 was used for descriptive and predictive statistics. Interviews were audio recorded, transcribed, and analyzed using a thematic, constructivist approach with consensus coding using NVivo 10.0. Field and interview notes collected during the observational study were aligned with themes identified through individual interviews.

Results

Of 150 survey respondents, 76% agreed or strongly agreed that antibiotics are overused in the ED, while half believed they personally did not overprescribe. Eighty-nine percent used a smartphone or tablet in the ED for antibiotic prescribing decisions. Several significant differences were found between attending and resident physicians. Interview analysis identified 42 codes aggregated into the following themes: (1) resource and environmental factors that affect care; (2) access to and quality of care received outside of the ED consult; (3) patient-provider relationships; (4) clinical inertia; and (5) local knowledge generation. The observational study revealed limited patient understanding of antibiotic use. Providers relied heavily upon diagnostics and provided limited education to patients. Most patients denied a priori expectations of being prescribed antibiotics.

Conclusions

Patient, provider, and healthcare system factors should be considered when designing interventions to improve antimicrobial stewardship in the ED setting.

Infect Control Hosp Epidemiol 2014;35(9):1114-1125
‘All the Trimmings?’: The Transfer of Theatre to Television in Adaptations of Shakespeare Stagings
Authors: Wyver John
Published: July 2014

Since 1937, almost fifty British television productions of Shakespeare have been adapted from specific theatre stagings. This article surveys the history of these transmissions of previously staged performances of Shakespeare. It outlines the changing ways in which these adaptations have been important to television and it explores ideas about their status and effectivity. It argues that rather than being seen simply as ‘documentation’ and as the inferior traces of theatrical originals, these productions might more productively be regarded as doubled adaptations. That is, they can be understood as adaptations for the screen of a text—a staging of a Shakespeare play—that was previously, as a staged performance, an adaptation in itself. The interplay between the televisual, theatrical, and cinematic elements of these adaptations is considered and the history is set within in the context of the rapidly developing contemporary form of live cinema, exemplified by National Theatre Live and Live from Stratford-upon-Avon, which recreates as spectacle in a social context many of the approaches and concerns of television’s adaptations of Shakespeare stagings.
Let's Talk About the Money: Spousal Communication, Expenditures, and Farm Production
Authors: Chen Joyce J. , Collins LaPorchia A.
Published: July 2014

A burgeoning body of literature highlights asymmetric information among household members. However, little is known about the source of the asymmetry and its effect on efficiency. Using a unique survey of Ghanaian households, we examine the accuracy of spousal cross reports and the effect of discrepancies on farm production. We find that information problems pertain to scale (the quantity of resources) and scope (the distribution of resources), as well as allocation decisions on the margin (Engel curves). Moreover, we find that information asymmetries lead to inefficiency in production, and the effect is equivalent to about 15% of the variation across households.
Monte Carlo algorithms for Brownian phylogenetic models
Authors: Horvilleur Benjamin , Lartillot Nicolas
Published: July 2014

Motivation : Brownian models have been introduced in phylogenetics for describing variation in substitution rates through time, with applications to molecular dating or to the comparative analysis of variation in substitution patterns among lineages. Thus far, however, the Monte Carlo implementations of these models have relied on crude approximations, in which the Brownian process is sampled only at the internal nodes of the phylogeny or at the midpoints along each branch, and the unknown trajectory between these sampled points is summarized by simple branchwise average substitution rates.

Results : A more accurate Monte Carlo approach is introduced, explicitly sampling a fine-grained discretization of the trajectory of the (potentially multivariate) Brownian process along the phylogeny. Generic Monte Carlo resampling algorithms are proposed for updating the Brownian paths along and across branches. Specific computational strategies are developed for efficient integration of the finite-time substitution probabilities across branches induced by the Brownian trajectory. The mixing properties and the computational complexity of the resulting Markov chain Monte Carlo sampler scale reasonably with the discretization level, allowing practical applications with up to a few hundred discretization points along the entire depth of the tree. The method can be generalized to other Markovian stochastic processes, making it possible to implement a wide range of time-dependent substitution models with well-controlled computational precision.

Availability : The program is freely available at www.phylobayes.org

Contact : nicolas.lartillot@univ-lyon1.fr
Spawning site fidelity by Atlantic cod (Gadus morhua) in the Gulf of Maine: implications for population structure and rebuilding
Authors: Zemeckis Douglas R. , Hoffman William S. , Dean Micah J. , Armstrong Michael P. , Cadrin Steven X.
Published: July 2014

Rebuilding the Gulf of Maine stock of Atlantic cod (Gadus morhua) has been much slower than expected. An important source of scientific uncertainty contributing to the difficulties in managing rebuilding has been the lack of understanding of cod population structure. Previous research indicates that the stock functions as a metapopulation that is made up of multiple subpopulations and many finer-scale spawning components. This study investigated fine-scale, multiyear spawning site fidelity by a spring-spawning component of Atlantic cod in the western Gulf of Maine. Movements of acoustically tagged cod (n = 63) with respect to a known spawning site were tracked using passive acoustic telemetry. A large proportion (38–67%) of tagged cod exhibited spawning site fidelity between 2010 and 2012. After adjusting for fishing mortality, natural mortality, and skipped spawning, the estimated rate of spawning site fidelity ranged between 47 and 95% in 2011. Multiyear spawning site fidelity was also observed, with individuals being tracked for up to four consecutive spawning seasons. Spawning site fidelity serves as one of the multiple mechanisms that contribute to the formation and maintenance of the observed metapopulation structure. Spawning site fidelity also reduces the reproductive connectivity among spawning sites, thus delaying both recolonization of abandoned spawning sites and stock rebuilding. Future stock assessment models and fishery management plans that incorporate the metapopulation structure of cod in the Gulf of Maine are expected to be more effective at preventing continued declines in spawning diversity and promoting rebuilding.
Incorporating the spatial access priorities of fishers into strategic
conservation planning and marine protected area design: reducing cost and
increasing transparency
Authors: Yates K. L. , Schoeman D. S.
Published: July 2014

Marine protected areas (MPAs) are increasingly used to address multiple marine management needs, and the incorporation of stakeholders into the MPA planning and designation processes is considered vital for success. Commercial fishers are often the stakeholder group most directly affected by spatial restrictions associated with MPAs, and the success of MPAs often depends, at least in part, on the behaviours and attitudes of fishers. MPA planning processes that incorporate fishers, and minimize the negative impact of MPA designation on the fishing community, should therefore have a greater chance of success. Here, the incorporation of both quantitative and qualitative fisher-derived data in MPA planning is investigated using strategic conservation planning software and multi-scenario analysis. We demonstrate the use of spatial access priority data as a cost layer, and suggest a process for incorporating fishers' MPA suggestions into planning scenarios in a transparent, but flexible, way. Results show that incorporating fisher-derived data, both quantitative and qualitative, can significantly reduce the cost of MPA planning solutions: enabling the development of MPA network designs that meet conservation targets with less detrimental impact to fishing community. Incorporating fishers and fisher-derived data in MPA planning processes can improve both the efficiency and defensibility of planning outcomes, as well as contribute to reducing potential conflicts between biodiversity conservation and the fishing industry.
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome
Authors: Thévenin Annelyse , Ein-Dor Liat , Ozery-Flato Michal , Shamir Ron
Published: July 2014

Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clustering of genes by function, except for few concrete functional groups. We set out to check systematically if there is a relation between gene function and gene organization in the human genome. We test this question for three types of functional groups: pairs of interacting proteins, complexes and pathways. We find a significant concentration of functional groups both in terms of their distance within the same chromosome and in terms of their dispersal over several chromosomes. Moreover, using Hi-C contact map of the tendency of chromosomal segments to appear close in the 3D space of the nucleus, we show that members of the same functional group that reside on distinct chromosomes tend to co-localize in space. The result holds for all three types of functional groups that we tested. Hence, the human genome shows substantial concentration of functional groups within chromosomes and across chromosomes in space.
Suppression of Fusarium Wilt Caused by Fusarium oxysporum f. sp. niveum Race 2 on Grafted Triploid Watermelon
Authors: Keinath Anthony P. , Hassell Richard L.
Published: July 2014

Fusarium wilt of watermelon, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. niveum race 2, is a serious, widespread disease present in major watermelon-growing regions of the United States and other countries. ‘Fascination,’ a high yielding triploid resistant to race 1, is grown in southeastern states in fields that contain a mixture of races 1 and 2. There is some benefit to using cultivars with race 1 resistance in such fields, even though Fascination is susceptible to Fusarium wilt caused by race 2. Experiments in 2012 and 2013 were done in fields infested primarily with race 2 and a mixture of races 1 and 2, respectively. Fascination was grafted onto four rootstock cultivars: bottle gourd (Lagenaria siceraria) ‘Macis’ and ‘Emphasis’ and interspecific hybrid squash (Cucurbita maxima× C. moschata) ‘Strong Tosa’ and ‘Carnivor.’ Nongrafted and self-grafted Fascination were used as susceptible control treatments. In both experiments, mean incidence of plants with symptoms of Fusarium wilt was ≥52% in the susceptible control treatments and ≤6% on the grafted rootstocks. Disease incidence did not differ between rootstock species or cultivars. In both years, Fascination grafted onto Strong Tosa and Macis produced more marketable-sized fruit than the susceptible control treatments. Grafted Emphasis and Carnivor also produced more fruit than the control treatments in 2012. The cucurbit rootstocks suppressed Fusarium wilt caused by race 2 and increased marketable yield of triploid watermelon grown in infested soil.
First Report of Aster Yellows Phytoplasma in Soybean in Michigan
Authors: Mollov D. , Chilvers M. I. , Jacobs J. L.
Published: July 2014

During the summer of 2012, soybean plants in a commercial field in Clinton County, Michigan, exhibited symptoms characteristic of phytoplasmal diseases (1,2). Symptoms included extensive top dieback, stunting, purple stem surfaces, internal necrosis, leaf vein discoloration, and bud proliferation. Approximately 80% of plants in a half hectare along the southern edge of the field were symptomatic, although the majority of plants in the 4-ha field appeared symptomless. Total genomic DNA was extracted from one symptomatic and one asymptomatic leaf sample using a Qiagen DNeasy Plant Mini Kit (Qiagen, Germantown, MD) according to manufacturer's instructions. The DNA was used as template in direct PCR primed by the phytoplasma-universal primers P1/P7 followed by nested PCR primed by P1/AYint (3). Reactions containing template DNA from the symptomatic plant yielded ribosomal RNA gene amplicons of 1.8 kbp (P1/P7-primed) and 1.6 kbp (P1/AYint-primed), respectively. Reactions containing template DNA from the asymptomatic plant or water did not yield amplicons. The products of PCRs primed by P1/P7 were purified using PureLink PCR Purification kit (Life Technologies, Carlsbad, CA) and cloned in a pGem T-Easy vector system (Promega, Madison, WI). Three separate clones were sequenced using the sequencing primers M13For, M13Rev, SAYF nt 755, (5′-AAAGCGTGGGGAGCAAACAG), and SAYR nt 1159, (5′-TTTGACGTCGTCCCCACCTT). The sequences of all three clones were identical. A consensus (Sequencher 4.1, Gene Codes Corporation, Ann Arbor, MI) nucleotide sequence of 1,830 bp was deposited in GenBank under the accession number KF528320. A BLASTn similarity search revealed that the sequence shared 100% identity to rDNA of aster yellows phytoplasma (AF222063). Additionally, analysis of the 16Sr group/subgroup classification, based on in silico RFLP analyses using iPhyClassifier (4), indicated that the soybean phytoplasma is a member of subgroup 16SrI-B aster yellows phytoplasma subgroup. In a phylogenic tree deduced using the neighbor joining algorithm, the phytoplasma consensus sequence obtained from soybean in Michigan clustered with other group 16SrI (aster yellows phytoplasma) strains. While aster yellows phytoplasma has been previously reported in soybean in Wisconsin (2), to our knowledge, this is the first report of aster yellows in soybean in Michigan.

References: (1) C. R. Grau et al. Compendium of Soybean Diseases, 4th ed. G. L. Hartman et al., eds. American Phytopathological Society, St. Paul, MN, 1999. (2) M. E. Lee et al. Can. J. Plant Pathol. 24:125, 2002. (3) C. D. Smart et al. Appl. Env. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
First Report of Grapevine leafroll-associated virus-2 and -3 in Texas Vineyards
Authors: Jones T. J. , Westover F. , Nita M.
Published: July 2014

Grapevine leafroll disease (GLD), caused by the grapevine leafroll-associated viruses (GLRaVs, family Closteroviridae) is an important disease in all grapevine-growing regions of the world (2). It negatively affects vine vigor, fruit yield, and grape quality (e.g., sugar accumulation) (3). Typical disease symptoms include downward rolling of grape leaves accompanied by interveinal reddening in red-fruited varieties and interveinal chlorosis in white-fruited varieties (2). The state of Texas currently has over 275 commercial vineyards and acreage under grape production is expanding. Currently, there is limited information on the presence of either GLRaV-2 (genus Closterovirus) or GLRaV-3 (genus Ampelovirus) in this state. During the 2012 season, 19 individual, symptomatic grapevines (13 cv. Lenoir and 6 cv. Blanc du Bois) were sampled (14 petioles per vine) from one vineyard site in Richards, TX. Total nucleic acid was extracted from the samples as described before (5) and tested by RT-PCR using species specific primers to amplify a 334-bp fragment of the HSP70h gene of GLRaV-2 (L2 F: 5′-ATAATTCGGCGTACATCCCCACTT-3′ and U2 R: 5′-GCCCTCCGCGCAACTAATGACAG-3′) (1) and a 541-bp fragment of the HSP70h gene of GLRaV-3 (LC1 F: 5′-CGCTAGGGCTGTGGAAGTATT-3′ and LC2 R: 5′-GTTGTCCCGGGTACCAGATAT-3′) (4). Samples were also subjected to triple (TAS) and double (DAS) antibody sandwich ELISA for GLRaV-2 and GLRaV-3 using commercially available antibody test kits (AC Diagnostics, Fayetteville, AR). Five samples tested positive for GLRaV-2 and one for GLRaV-3, all from the variety Lenoir with no incidences of mixed infection. In addition to the RT-PCR and ELISA, the presence of GLRaV-2 and GLRaV-3 was confirmed by direct sequencing of select RT-PCR products, which was purified using the QIAquick PCR Purification kit (Qiagen Inc., CA). The sequencing took place at the Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA. GLRaV-2 isolate TX12 (GenBank Accession No. KF417612) and GLRaV-3 isolate TX9 (KJ545571) shared 85 to 100% and 94 to 100% nucleotide identity and 74 to 100% and 82 to 100% amino acid identity, respectively, with previously reported isolates from around the world. All samples tested negative for GLRaV-1, -4, -4 strain 5, and -4 strain 9 (4), suggesting that some of the symptomatic vines may have a different disease or abiotic disorder, such as a nutrient deficiency. To our knowledge, this is the first report of GLRaV-2 and GLRaV-3 in the state of Texas.

References: (1) N. Bertazzon and E. Angelini. J. Plant Pathol. 86:283, 2004. (2) M. Fuchs et al. Plant Dis. 93:395, 2009. (3) L. Kovacs et al. Am. J. Enol. Vitic. 52:254, 2001. (4) F. Osman et al. J. Virol. Methods. 141:22, 2007. (5) A. Rowhani et al. Proc. ICVG (Adelaide). 13:82, 2000.
Selected Pacific Northwest Crops as Hosts of Pratylenchus neglectus and P. thornei
Authors: Smiley Richard W. , Yan Guiping , Gourlie Jennifer A.
Published: July 2014

Thirty crop species and cultivars were assayed in the greenhouse for efficiency as hosts of Pratylenchus neglectus and P. thornei. Hosting ability ratings were assigned using the ratio of final versus initial nematode density and also by comparing the final nematode density to that of a susceptible wheat control. Good hosts of both Pratylenchus spp. included oat ‘Monida’, chickpea ‘Myles’, and lentil ‘Athena’ and ‘Morton’. Good hosts of P. neglectus but not of P. thornei included 10 Brassica spp. (5 canola, 2 mustard, and 3 camelina cultivars), chickpea ‘Sierra’, sudangrass ‘Piper’, and sorghum/sudangrass hybrid ‘Greentreat Plus’. Good hosts of P. thornei but not of P. neglectus included lentil ‘Skyline’ and pea ‘Granger’, ‘Journey’, and ‘Universal’. Poor or minor hosts of both Pratylenchus spp. included chickpea ‘Dwelley’, pea ‘Badminton’, safflower ‘Gila’, ‘Girard’, and ‘KN 144’, sunflower ‘2PD08’, flax ‘Pembina’, eastern gamagrass ‘Pete’, and switchgrass ‘Blackwell’. Results of these assays will provide guidance for improving crop rotation and cultivar selection efficiencies.
Characterization by Deep Sequencing of Prunus virus T, a Novel Tepovirus Infecting Prunus Species
Authors: Marais Armelle , Faure Chantal , Mustafayev Eldar , Barone Maria , Alioto Daniela , Candresse Thierry
Published: July 2014

Double-stranded RNAs purified from a cherry tree collected in Italy and a plum tree collected in Azerbaijan were submitted to deep sequencing. Contigs showing weak but significant identity with various members of the family Betaflexiviridae were reconstructed. Sequence comparisons led to the conclusion that the viral isolates identified in the analyzed Prunus plants belong to the same viral species. Their genome organization is similar to that of some members of the family Betaflexiviridae, with three overlapping open reading frames (RNA polymerase, movement protein, and capsid protein). Phylogenetic analyses of the deduced encoded proteins showed a clustering with the sole member of the genus Tepovirus, Potato virus T (PVT). Given these results, the name Prunus virus T (PrVT) is proposed for the new virus. It should be considered as a new member of the genus Tepovirus, even if the level of nucleotide identity with PVT is borderline with the genus demarcation criteria for the family Betaflexiviridae. A reverse-transcription polymerase chain reaction detection assay was developed and allowed the identification of two other PrVT isolates and an estimate of 1% prevalence in the large Prunus collection screened. Due to the mixed infection status of all hosts identified to date, it was not possible to correlate the presence of PrVT with specific symptoms.
Too much of a good thing: resource provisioning alters infectious disease dynamics in wildlife
Authors: Becker Daniel J. , Hall Richard J.
Published: July 2014

Provisioning of abundant food resources in human-altered landscapes can have profound effects on wildlife ecology, with important implications for pathogen transmission. While empirical studies have quantified the effects of provisioning on host behaviour and immunology, the net interactive effect of these components on host–pathogen dynamics is unknown. We use simple compartmental models to investigate how provisioning-induced changes to host demography, contact behaviour and immune defence influence pathogen invasion and persistence. We show that pathogen invasion success and equilibrium prevalence depend critically on how provisioning affects host immune defence and that moderate levels of provisioning can lead to drastically different outcomes of pathogen extinction or maximizing prevalence. These results highlight the need for further empirical studies to fully understand how provisioning affects pathogen transmission in urbanized environments.
Optimal orientation in flows: providing a benchmark for animal movement strategies
Authors: McLaren James D. , Shamoun-Baranes Judy , Dokter Adriaan M. , Klaassen Raymond H. G. , Bouten Willem
Published: July 2014

Animal movements in air and water can be strongly affected by experienced flow. While various flow-orientation strategies have been proposed and observed, their performance in variable flow conditions remains unclear. We apply control theory to establish a benchmark for time-minimizing (optimal) orientation. We then define optimal orientation for movement in steady flow patterns and, using dynamic wind data, for short-distance mass movements of thrushes (
Turdus
sp.) and 6000 km non-stop migratory flights by great snipes,
Gallinago media.
Relative to the optimal benchmark, we assess the efficiency (travel speed) and reliability (success rate) of three generic orientation strategies: full compensation for lateral drift, vector orientation (single-heading movement) and goal orientation (continually heading towards the goal). Optimal orientation is characterized by detours to regions of high flow support, especially when flow speeds approach and exceed the animal's self-propelled speed. In strong predictable flow (short distance thrush flights), vector orientation adjusted to flow on departure is nearly optimal, whereas for unpredictable flow (inter-continental snipe flights), only goal orientation was near-optimally reliable and efficient. Optimal orientation provides a benchmark for assessing efficiency of responses to complex flow conditions, thereby offering insight into adaptive flow-orientation across taxa in the light of flow strength, predictability and navigation capacity.
Surface folding in metals: a mechanism for delamination wear in sliding
Authors: Mahato Anirban , Guo Yang , Sundaram Narayan K. , Chandrasekar Srinivasan
Published: July 2014

Using high-resolution,
in situ
imaging of a hard, wedge-shaped model asperity sliding against a metal surface, we demonstrate a new mechanism for particle formation and delamination wear. Damage to the residual surface is caused by the occurrence of folds on the free surface of the prow-shaped region ahead of the wedge. This damage manifests itself as shallow crack-like features and surface tears, which are inclined at very acute angles to the surface. The transformation of folds into cracks, tears and particles is directly captured. Notably, a single sliding pass is sufficient to damage the surface, and subsequent passes result in the generation of platelet-like wear particles. Tracking the folding process at every stage from surface bumps to folds to cracks/tears/particles ensures that there is no ambiguity in capturing the mechanism of wear. Because fold formation and consequent delamination are quite general, our findings have broad applicability beyond wear itself, including implications for design of surface generation and conditioning processes.
The sliding contact of a rigid wavy surface with a viscoelastic half-space
Authors: Menga N. , Putignano C. , Carbone G. , Demelio G. P.
Published: July 2014

In this paper, the contact of a rigid sinusoid sliding on a viscoelastic half-space is studied. The solution of the problem is obtained by following the path drawn by Hunter for cylindrical contacts. Results show that depending on the remote applied load, a transition from full contact conditions to partial contact may occur depending on the sliding velocity. This effect, which is not observed in smooth single asperity contacts, is related to the viscoelastic stiffening of the material and to the periodicity of the contacts. Frictional properties as well as contact area, displacement and pressure distributions are discussed in detail.
Demography can favour female-advantageous alleles
Authors: Harts Anna M. F. , Schwanz Lisa E. , Kokko Hanna
Published: July 2014

When female fecundity is relatively independent of male abundance, while male reproduction is proportional to female abundance, females have a larger effect on population dynamics than males (i.e. female demographic dominance). This population dynamic phenomenon might not appear to influence evolution, because male and female genomes still contribute equally much to the next generation. However, here we examine two evolutionary scenarios to provide a proof of principle that spatial structure can make female demographic dominance matter. Our two simulation models combine dispersal evolution with local adaptation subjected to intralocus sexual conflict and environmentally driven sex ratio biases, respectively. Both models have equilibria where one environment (without being intrinsically poorer) has so few reproductive females that trait evolution becomes disproportionately determined by those environments where females survive better (intralocus sexual conflict model), or where daughters are overproduced (environmental sex determination model). Surprisingly, however, the two facts that selection favours alleles that benefit females, and population growth is improved when female fitness is high, together do not imply that all measures of population performance are improved. The sex-specificity of the source–sink dynamics predicts that populations can evolve to fail to persist in habitats where alleles do poorly when expressed in females.