bluuebunny/crossref_metadata_2025 huggingface dataset:
Quality assurance: a vital need in ecological monitoring.
Authors: Ferretti M.
Published: August 2014

Much of our knowledge about the status of and changes in ecological systems and their response to environmental stresses has originated from ecological monitoring. However, concern exists about the ability of monitoring to provide 'good' data. The value of monitoring is often questioned and monitoring itself is seen as an exercise with little contact with true science. Such concerns are justified given several examples of abuse and misuse of monitoring data and failure in documenting errors and flaws. When data are flawed, even the most sophisticated statistical and modelling technique is useless. As a consequence, there are risks that the environmental policy decision-making process may be severely compromised, leading to wrong decisions and additional costs to society. Data quality is therefore essential for decision quality. However, data quality goes beyond the traditional perception of metrological quality, and the process of obtaining 'good' data needs to consider all the steps involved in the monitoring. Ecological monitoring cannot survive outside a rigorous scientific context, and a comprehensive quality assurance framework is necessary to drive the design and the implementation of a monitoring programme.
Quantitative polymerase chain reaction for the detection of organisms in soil.
Authors: Bilodeau G. J.
Published: August 2014

Detection and quantification of soil organisms using traditional methods (culture, plating and microscopy) are difficult and do not always allow identification. In the last decade, real-time quantitative polymerase chain reaction (qPCR) has allowed rapid, sensitive, specific and high-throughput detection and quantification of organisms. For example, in plant health, this new method helps in the management of plant disease in agriculture and forestry. However, direct DNA detection in soil is often difficult because of PCR inhibitors, low inoculum density and inadequate sampling techniques. This review presents diverse real-time qPCR methods for the detection and quantification of soil-borne organisms (mainly pathogenic organisms), addresses difficulties using real-time qPCR for quantification of organisms in soil and presents solutions and methods to overcome these challenges. Examples of utilizing real-time qPCR on different types of organisms such as fungi, bacteria, nematodes, viruses, plants and for soil diversity are presented along with explanations of computational techniques for the estimation of organism levels in soil. The different applications of quantification are discussed with regard to detection and management, biocontrol recovery, genotyping of organism and population studies and ecological biodiversity. The importance of having an internal control and quality DNA for accurate quantification and high copy-number for sensitivity is discussed.
Food security: the role of effective agrobiodiversity management.
Authors: Lenné J. M. , Wood D.
Published: August 2014

Over the next 30 years, global agriculture will be faced with the daunting problem of feeding an additional 2-3 billion people with less water, less energy and less fertilizer from the same land base. However, agriculture has surmounted equal or larger problems in the past through a series of revolutionary advances, many of which have depended on improved management of crop and animal diversity and their interactions with the associated beneficial and harmful biodiversity. Future global food security is therefore firmly anchored in sound science-based management of this agrobiodiversity. Knowledgeable, practical and realistic management of agrobiodiversity by farmers and scientists is the most important toolbox available for significantly increasing global food production. Enhanced policy support and significant increases in donor investment will be essential for effective growth in agricultural productivity and global food security.
Using near-infrared spectroscopy to predict postharvest quality.
Authors: Cayuela Sánchez J. A.
Published: August 2014

Near-infrared spectroscopy offers great potential for controlling postharvest quality attributes of fruits and vegetables. It constitutes a very useful tool to ensure their acceptability and characterizing their nutritional properties. The literature regarding its use for postharvest quality parameters prediction on fresh fruit and vegetables, has been reviewed. The aspects of quality that can be measured by near-infrared spectroscopy (NIRS), its evolution, research on different products and most important areas for action, are highlighted. Desirable criteria for evaluating the reliability of the models and spectrometer features such as portability are discussed. Likely events in the evolution of online and portable NIRS in the near future are suggested.
Increasing the vitamin E content of food by in-plant production.
Authors: Farré G. , Zorrilla U. , Zhu C. F. , Christou P. , Capell T.
Published: August 2014

Vitamin E is a group of eight, lipid-soluble molecules known as tocochromanols, featuring a conserved head group and an aliphatic side chain. They are produced by plants and some cyanobacteria, and act as free-radical scavengers in mammals to prevent lipid oxidation. The different isomers of vitamin E can be classed as tocopherols or tocotrienols depending on the chemical conformation of the side chain. The natural isomer α-tocopherol (RRR-α-tocopherol) is more active than synthetic vitamin E, making it the most effective natural form of the vitamin. The composition of vitamin E differs widely among plant species and varieties, and many crops have been bred or engineered to increase their vitamin E levels. In this review, we discuss strategies to increase vitamin E levels and alter the vitamin E composition in plants, and present case studies that demonstrate the impact of these strategies in different crops.
Molecular isolation and functional characterization of host factors required in the virus infection cycle for disease control in plants.
Authors: Wang AiMing Wang AiMing
Published: August 2014

Plant viral infection results in a multi-billion dollar economic loss worldwide each year. The use of genetic resistance is the most effective and sustainable approach to the control of plant viral diseases. However, owing to the lack of natural resistance genes, a single devastating viral pathogen often becomes a significant limiting factor in crop production. All plant viruses have a small viral genome that encodes a limited number of viral proteins. They must depend on host gene products (host factors) to complete their life cycle. Mutation, silencing or down-regulation of host factor gene(s) may lead to recessively inherited resistance to viruses. This is a major driving force for the molecular identification and functional characterization of host factors essential in virus infections. Potyviruses represent over 30% of all known plant viruses and constitute the largest plant virus group. Many agriculturally important viruses are potyviruses. In the last decade, several potyviral host factor genes including the well-known eIF4E or eIF(iso)4E gene have been molecularly identified. In this review, I will summarize research progress in molecular understanding of potyviral infection processes, and discuss manipulation of the identified host factors against potyviruses.
Comparing nutritional content of fruits, vegetables and juices from organic and conventional crops.
Authors: Gąstoł M. , Domagala-Świątkiewicz I.
Published: August 2014

The nutritional quality of food produced by organic farming in comparison with conventional farming is a current topic that focuses interest and generates discussion. This paper presents a review of the relevant literature of comparative studies on organic and conventional food. In line with several reports on organic fruit and vegetable quality, the data obtained from a wide evaluation of Polish organic versus conventional crops are compared and discussed. This comparative study covered 33 neighbouring pairs of organic/conventional fields with six evaluated species. The data on dry matter, sugar, organic acids and polyphenols content are provided, along with a special respect to mineral content of fruit and vegetable juices. Some issues on the methodological aspects of such comparative studies are presented.
Effects of postharvest handling and storage on antioxidant activity of berry fruits.
Authors: Cantin C. M. , Echeverria G.
Published: August 2014

Berries are a rich source of natural polyphenolics and antioxidant compounds, and they are recognized as functional foods. Although they are best eaten freshly picked, some postharvest conditions and treatments are necessary in order to extend their short shelf life. Postharvest handling and storage have an evident effect on the nutraceutical properties of small berries. This review focuses on the effects of the main postharvest operations applied to berries such as storage temperature, controlled atmosphere, edible coatings, UV irradiation, antimicrobial compounds, heat treatments and washing disinfection, particularly on the antioxidant activity of the fruit. Further, we conclude with the importance of selecting postharvest operations which minimize the losses of antioxidant compounds while maintaining the consumer satisfaction. Also, we underline the importance of informing consumers regarding the nutraceutical composition of fruit and the effect of domestic practices on these compounds of human health interest that are naturally present in berry fruits, and suggest future research approaches.
Developments in diagnosis and control of bovine paratuberculosis.
Authors: Nielsen S. S.
Published: August 2014

Bovine paratuberculosis can be costly to farmers who, as a consequence, may be interested in control of the causative agent,
Mycobacterium avium
subsp.
paratuberculosis
(MAP). Between-herd spread is primarily due to movement of MAP-infected livestock, and within-herd transmission most often occurs when susceptible calves are exposed to the faeces of infectious adult cattle. This review provides an update on options to control MAP infections via the use of diagnostics, with an emphasis on dairy cattle. Control of MAP infections can be achieved through improved hygienic measures and reducing the exposure of susceptible animals to the milk and faeces of infected animals. However, cost-effectiveness may depend on labour costs, and strategic use of diagnostics may have certain appeals through the information provided. Current bulk tank milk tests are not deemed to have a role in MAP control, whereas other herd-level diagnostics can be useful to guide establishment of control schemes by estimating whether MAP infections are prevalent or not. Then, test strategies based on screenings using cow-level tests can be used to identify the majority of infectious animals. The proportion of detected infectious animals depends on the timing of testing. If test results are used for risk-based management, then it is of utmost importance that they are still valid when used. Test results 3-6 months old may have lost a significant part of their validity. However, more research on the validity of test results over time to determine the infectiousness of animals should be carried out to enable the design of better test strategies.
Oral administration of the AYA strain ofLactobacillus plantarummodulates expression of immunity-related genes in the murine Peyer’s patch: a DNA microarray analysis
Authors: Kikuchi Yosuke , Toyoda Tsudoi , Ishijima Tomoko , Abe Keiko , Nakai Yuji , Fukudome Shin-ichi
Published: August 2014

We performed comprehensive transcriptome analysis of Peyer’s patches to elucidate the effects of oral administration of Lactobacillus plantarum strain AYA in mice. Using microarray analysis, we identified 124 upregulated and 144 downregulated genes for four weeks after the start of dietary supplementation with AYA. Gene Ontology analysis revealed that the genes for immune function were enriched in the upregulated gene set.
Assessing pupils at the age of 16 in England – approaches for effective examinations
Authors: He Qingping , Opposs Dennis , Glanville Matthew , Lampreia‐Carvalho Fatima
Published: August 2014

In England, pupils aged 16 take the General Certificate of Secondary Education (GCSE) examinations for a range of subjects. The current assessment models for GCSE include a two‐tier structure for some subjects and a non‐tier model for the others. The tiered subjects have a higher tier designed for high achieving pupils and a lower tier for low achieving pupils. The higher tier paper is targeted at grades A∗–D (with A∗ the highest grade available), while the lower tier paper at grades C–G (with G the lowest grade). The UK government has proposed a comprehensive reform of GCSEs. It suggested that, with tiered papers, pupils are forced to choose between higher and lower tier papers, which will place a cap on the ambition of those entering for the lower tier. The government therefore suggests avoiding tiering in the reformed GCSEs when possible. This paper discusses the technical and equity issues with the use of tiered examinations in current GCSEs and reviews potential alternative assessment approaches for effective differentiation between pupils for the reformed GCSEs.
From Europeanization to European Construction
Authors: Rabeharisoa Vololona , O'Donovan Órla
Published: August 2014

In this article, we examine how European patients' organizations (EPOs) contribute to moving patient advocacy beyond national level organizing and acting. In contrast to Europeanization studies, our contention is that EPOs are not content merely to bring national claims up to the European level nor simply enrich national debates with European issues. Rather, we argue that EPOs engage in a compounded multilevel construction of patients as ‘European individuals’ and of their conditions as matters of concern for Europe. Based on an analysis of the projects, pronouncements, and politics of three EPOs – European Organization on Rare Diseases, Alzheimer Europe, and Attention Deficit Hyperactivity Disorder Europe – we explore how they form European communities of patients and give shape to health issues they deem important to address at European level. We show that EPOs' involvement in the ongoing construction of Europe relies on their capacities to collect, format, and circulate comparative facts, figures, and data on the functioning of domestic health systems, drawn notably on their members' experiences. This helps them to raise discussions on the need for European health-care policies which articulate a ‘Europe of markets’ and a ‘social Europe’ to the benefit of the patients. We discuss the form of politics that this EPOs’ ‘evidence-based activism’, as we call it, entails, and conclude with a few thoughts on their influence on the making of European health-care policies.
The surprising dynamics of scaffolding proteins
Authors: Garbett Damien , Bretscher Anthony
Published: August 2014

The function of scaffolding proteins is to bring together two or more proteins in a relatively stable configuration, hence their name. Numerous scaffolding proteins are found in nature, many having multiple protein–protein interaction modules. Over the past decade, examples of scaffolding complexes long thought to be stable have instead been found to be surprisingly dynamic. These studies are scattered among different biological systems, and so the concept that scaffolding complexes might not always represent stable entities and that their dynamics can be regulated has not garnered general attention. We became aware of this issue in our studies of a scaffolding protein in microvilli, which forced us to reevaluate its contribution to their structure. The purpose of this Perspective is to draw attention to this phenomenon and discuss why complexes might show regulated dynamics. We also wish to encourage more studies on the dynamics of “stable” complexes and to provide a word of caution about how functionally important dynamic associations may be missed in biochemical and proteomic studies.
Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes
Authors: Curran David M. , Gilleard John S. , Wasmuth James D.
Published: August 2014

Motivation: Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies. The program uses a pattern of short sequence motifs to identify putative genes directly from the genome sequence. Using a large gene family as a test case, Figmop was found to be more sensitive and specific than a BLAST-based approach. The visualization used allows the validation of potential genes to be carried out quickly and easily, saving hours if not days from an analysis.

Availability and implementation: Source code of Figmop is freely available for download at https://github.com/dave-the-scientist , implemented in C and Python and is supported on Linux, Unix and MacOSX.

Contact:  curran.dave.m@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Orbital Lipomatosis: A Complication of Steroid Therapy in the Sweet Syndrome
Authors: Da Costa Gwendoline , Pare Arnaud , Sury Florent , Goga Dominque , Laure Boris
Published: August 2014

The description of a Sweet syndrome steroid dependant-induced orbital lipomatosis is reported. A 76-year-old-man with history of Sweet syndrome presented with severe bilateral proptosis (Hertel value, 25 mm) with decreased visual acuity and evoked potentials lengthened. A bilateral transpalpebral orbital decompression was performed by resection of intraorbital fat without bone removal. The surgery was uneventful. The volume of resected orbital fat was 15 ml for both sides. Proptosis reduction was 6 mm. Postoperative Hertel values were 19 mm, and evoked potentials were improved. The proptosis was managed successfully. Orbital lipectomy led to minimal sequelae and may be repeated if necessary in this case.
Improving Insulin Administration Through Redesigning Processes of Care: A Multidisciplinary Team Approach
Authors: Citty Sandra Wolfe , Zumberg Lisa , Chappell Justina
Published: August 2014

Objectives

This article describes a quality improvement project using a multidisciplinary team approach to improve the rate of errors of omission of preprandial subcutaneous coverage insulin orders.

Methods

A Diabetic Management Work Group was created to evaluate the system processes that affect success and failure of timely administration and documentation of preprandial coverage insulin, commonly referred to as sliding scale coverage. Data before and after the project were collected to evaluate the effectiveness of a process change through the bar code medication administration system, in which preprandial coverage insulin order sets were changed to eliminate errors of omission and improve documentation.

Results

A review of 833 random blood glucose measurements with corresponding short- or rapid-acting insulin coverage orders was conducted. A mean error of omission rate of 23.4% was identified with respect to coverage insulin that was clinically indicated by provider-ordered insulin set but not administered or documented in the electronic medication record. After process redesign and implementation, 951 blood glucose measurements with corresponding insulin coverage orders were randomly reviewed, and a mean of 10.7% of omission rate for coverage insulin administration was identified. This represented a decrease in omission of coverage insulin by 54% compared with preprocess improvement.

Conclusions

Decreased errors of omission as well as improved administration and documentation of coverage insulin were demonstrated by this multimodal process change. Scheduled standardized order sets, extensive nursing staff education, and enhanced efficiency of the existing process led to improved outcomes.
A Step Toward High Reliability: Implementation of a Daily Safety Brief in a Children’s Hospital
Authors: Saysana Michele , McCaskey Marjorie , Cox Elaine , Thompson Rachel , Tuttle Lora K. , Haut Paul R.
Published: August 2014

Objectives

Health care is a high-risk industry. To improve communication about daily events and begin the journey toward a high reliability organization, the Riley Hospital for Children at Indiana University Health implemented a daily safety brief.

Methods

Various departments in our children’s hospital were asked to participate in a daily safety brief, reporting daily events and unexpected outcomes within their scope of responsibility. Participants were surveyed before and after implementation of the safety brief about communication and awareness of events in the hospital. The length of the brief and percentage of departments reporting unexpected outcomes were measured.

Results

The analysis of the presurvey and the postsurvey showed a statistically significant improvement in the questions related to the awareness of daily events as well as communication and relationships between departments. The monthly mean length of time for the brief was 15 minutes or less. Unexpected outcomes were reported by 50% of the departments for 8 months.

Conclusions

A daily safety brief can be successfully implemented in a children’s hospital. Communication between departments and awareness of daily events were improved. Implementation of a daily safety brief is a step toward becoming a high reliability organization.
The enemy of my enemy is my friend: intraguild predation between invaders and natives facilitates coexistence with shared invasive prey
Authors: MacNeil Calum , Dick Jaimie T. A.
Published: August 2014

Understanding and predicting the outcomes of biological invasions is challenging where multiple invader and native species interact. We hypothesize that antagonistic interactions between invaders and natives could divert their impact on subsequent invasive species, thus facilitating coexistence. From field data, we found that, when existing together in freshwater sites, the native amphipod
Gammarus duebeni celticus
and a previous invader
G. pulex
appear to facilitate the establishment of a second invader, their shared prey
Crangonyx pseudogracilis.
Indeed, the latter species was rarely found at sites where each
Gammarus
species was present on its own. Experiments indicated that this may be the result of
G. d. celticus
and
G. pulex
engaging in more intraguild predation (IGP) than cannibalism; when the ‘enemy’ of either
Gammarus
species was present, that is, the other
Gammarus
species,
C. pseudogracilis
significantly more often escaped predation. Thus, the presence of mutual enemies and the stronger inter- than intraspecific interactions they engage in can facilitate other invaders. With some invasive species such as
C. pseudogracilis
having no known detrimental effects on native species, and indeed having some positive ecological effects, we also conclude that some invasions could promote biodiversity and ecosystem functioning.
Harry Smith CBE. 7 August 1921 — 10 December 2011
Authors: Rickinson Alan
Published: August 2014

Harry Smith was the person who, more than any other in the latter half of the twentieth century, prompted a renaissance of interest in the pathogenesis of microbial disease. A chemist turned microbiologist, his work on
Bacillus anthracis
, the causative agent of anthrax, led to the discovery in the serum of infected animals of the tripartite toxin that brings about the death of the host. These studies not only identified the first bacterial toxin, inspiring parallel work in related fields, but were seminally important in two further respects: first, they showed that toxins can be complexes of multiple components that, when studied individually, are nontoxic; and, second, they emphasized that research into infectious disease pathogenesis needs to focus on the biology of infection
in vivo
.
Interfacial and biological properties of the gradient coating on polyamide substrate for bone substitute
Authors: Huang Di , Niu Lulu , Wei Yan , Guo Meiqing , Zuo Yi , Zou Qin , Hu Yinchun , Chen Weiyi , Li Yubao
Published: August 2014

Fabrication of bioactive and mechanical matched bone substitutes is crucial for clinical application in bone defects repair. In this study, nano-hydroxyapatite/polyamide (nHA/PA) composite was coated on injection-moulded PA by a chemical corrosion and phase-inversion technique. The shear strength, gradient composition and pore structure of the bioactive coating were characterized. Osteoblast-like MG63 cells were cultured on pure PA and composite-coated PA samples. The cells' adhesion, spread and proliferation were determined using MTT assay and microscopy. The results confirm that the samples with the nHA/PA composite coating have better cytocompatibility and have no negative effects on cells. To investigate the
in vivo
biocompatibility, both pure PA and composite-coated PA cylinders were implanted in the trochlea of rabbit femurs and studied histologically, and the bonding ability with bone were determined using push-out tests. The results show that composite-coated implants exhibit better biocompatibility and the shear strength of the composite-coated implants with host bone at 12 weeks can reach 3.49 ± 0.42 MPa, which is significantly higher than that of pure PA implants. These results indicate that composite-coated PA implants have excellent biocompatibility and bonding abilities with host bone and they have the potential to be applied in repair of bone defects.
On the long-time integration of stochastic gradient systems
Authors: Leimkuhler B. , Matthews C. , Tretyakov M. V.
Published: August 2014

This article addresses the weak convergence of numerical methods for Brownian dynamics. Typical analyses of numerical methods for stochastic differential equations focus on properties such as the weak order which estimates the asymptotic (stepsize

h
→
0

) convergence behaviour of the error of finite-time averages. Recently, it has been demonstrated, by study of Fokker–Planck operators, that a non-Markovian numerical method generates approximations in the long-time limit with higher accuracy order (second order) than would be expected from its weak convergence analysis (finite-time averages are first-order accurate). In this article, we describe the transition from the transient to the steady-state regime of this numerical method by estimating the time-dependency of the coefficients in an asymptotic expansion for the weak error, demonstrating that the convergence to second order is exponentially rapid in time. Moreover, we provide numerical tests of the theory, including comparisons of the efficiencies of the Euler–Maruyama method, the popular second-order Heun method, and the non-Markovian method.
How modular structure can simplify tasks on networks: parameterizing graph optimization by fast local community detection
Authors: Bui-Xuan Binh-Minh , Jones Nick S.
Published: August 2014

By considering the task of finding the shortest walk through a Network, we find an algorithm for which the run time is not as
O
(2

n

), with
n
being the number of nodes, but instead scales with the number of nodes in a coarsened network. This coarsened network has a number of nodes related to the number of dense regions in the original graph. Since we exploit a form of local community detection as a preprocessing, this work gives support to the project of developing heuristic algorithms for detecting dense regions in networks: preprocessing of this kind can accelerate optimization tasks on networks. Our work also suggests a class of empirical conjectures for how structural features of efficient networked systems might scale with system size.
Maternal exposure to predator scents: offspring phenotypic adjustment and dispersal
Authors: Bestion Elvire , Teyssier Aimeric , Aubret Fabien , Clobert Jean , Cote Julien
Published: August 2014

Predation is a strong selective pressure generating morphological, physiological and behavioural responses in organisms. As predation risk is often higher during juvenile stages, antipredator defences expressed early in life are paramount to survival. Maternal effects are an efficient pathway to produce such defences. We investigated whether maternal exposure to predator cues during gestation affected juvenile morphology, behaviour and dispersal in common lizards (Zootoca vivipara). We exposed 21 gravid females to saurophagous snake cues for one month while 21 females remained unexposed (i.e. control). We measured body size, preferred temperature and activity level for each neonate, and released them into semi-natural enclosures connected to corridors in order to measure dispersal. Offspring from exposed mothers grew longer tails, selected lower temperatures and dispersed thrice more than offspring from unexposed mothers. Because both tail autotomy and altered thermoregulatory behaviour are common antipredator tactics in lizards, these results suggest that mothers adjusted offspring phenotype to risky natal environments (tail length) or increased risk avoidance (dispersal). Although maternal effects can be passive consequences of maternal stress, our results strongly militate for them to be an adaptive antipredator response that may increase offspring survival prospects.
Cryptic cuckoo eggs hide from competing cuckoos
Authors: Gloag Ros , Keller Laurie-Anne , Langmore Naomi E.
Published: August 2014

Interspecific arms races between cuckoos and their hosts have produced remarkable examples of mimicry, with parasite eggs evolving to match host egg appearance and so evade removal by hosts. Certain bronze-cuckoo species, however, lay eggs that are cryptic rather than mimetic. These eggs are coated in a low luminance pigment that camouflages them within the dark interiors of hosts' nests. We investigated whether cuckoo egg crypsis is likely to have arisen from the same coevolutionary processes known to favour egg mimicry. We added high and low luminance-painted eggs to the nests of large-billed gerygones (Gerygone magnirostris), a host of the little bronze-cuckoo (Chalcites minutillus). Gerygones rarely rejected either egg type, and did not reject natural cuckoo eggs. Cuckoos, by contrast, regularly removed an egg from clutches before laying their own and were five times more likely to remove a high luminance model than its low luminance counterpart. Given that we found one-third of all parasitized nests were exploited by multiple cuckoos, our results suggest that competition between cuckoos has been the key selective agent for egg crypsis. In such intraspecific arms races, crypsis may be favoured over mimicry because it can reduce the risk of egg removal to levels below chance.
Genetic elimination of field-cage populations of Mediterranean fruit flies
Authors: Leftwich Philip T. , Koukidou Martha , Rempoulakis Polychronis , Gong Hong-Fei , Zacharopoulou Antigoni , Fu Guoliang , Chapman Tracey , Economopoulos Aris , Vontas John , Alphey Luke
Published: August 2014

The Mediterranean fruit fly (medfly,
Ceratitis capitata
Wiedemann) is a pest of over 300 fruits, vegetables and nuts. The sterile insect technique (SIT) is a control measure used to reduce the reproductive potential of populations through the mass release of sterilized male insects that mate with wild females. However, SIT flies can display poor field performance, due to the effects of mass-rearing and of the irradiation process used for sterilization. The development of female-lethal RIDL (release of insects carrying a dominant lethal) strains for medfly can overcome many of the problems of SIT associated with irradiation. Here, we present life-history characterizations for two medfly RIDL strains, OX3864A and OX3647Q. Our results show (i) full functionality of RIDL, (ii) equivalency of RIDL and wild-type strains for life-history characteristics, and (iii) a high level of sexual competitiveness against both wild-type and wild-derived males. We also present the first proof-of-principle experiment on the use of RIDL to eliminate medfly populations. Weekly releases of OX3864A males into stable populations of wild-type medfly caused a successive decline in numbers, leading to eradication. The results show that genetic control can provide an effective alternative to SIT for the control of pest insects.
Facial fluctuating asymmetry is not associated with childhood ill-health in a large British cohort study
Authors: Pound Nicholas , Lawson David W. , Toma Arshed M. , Richmond Stephen , Zhurov Alexei I. , Penton-Voak Ian S.
Published: August 2014

The idea that symmetry in facial traits is associated with attractiveness because it reliably indicates good physiological health, particularly to potential sexual partners, has generated an extensive literature on the evolution of human mate choice. However, large-scale tests of this hypothesis using direct or longitudinal assessments of physiological health are lacking. Here, we investigate relationships between facial fluctuating asymmetry (FA) and detailed individual health histories in a sample (n= 4732) derived from a large longitudinal study (Avon Longitudinal Study of Parents and Children) in South West England. Facial FA was assessed using geometric morphometric analysis of facial landmark configurations derived from three-dimensional facial scans taken at 15 years of age. Facial FA was not associated with longitudinal measures of childhood health. However, there was a very small negative association between facial FA and IQ that remained significant after correcting for a positive allometric relationship between FA and face size. Overall, this study does not support the idea that facial symmetry acts as a reliable cue to physiological health. Consequently, if preferences for facial symmetry do represent an evolved adaptation, then they probably function not to provide marginal fitness benefits by choosing between relatively healthy individuals on the basis of small differences in FA, but rather evolved to motivate avoidance of markers of substantial developmental disturbance and significant pathology.
Costs for switching partners reduce network dynamics but not cooperative behaviour
Authors: Bednarik Peter , Fehl Katrin , Semmann Dirk
Published: August 2014

Social networks represent the structuring of interactions between group members. Above all, many interactions are profoundly cooperative in humans and other animals. In accordance with this natural observation, theoretical work demonstrates that certain network structures favour the evolution of cooperation. Yet, recent experimental evidence suggests that static networks do not enhance cooperative behaviour in humans. By contrast, dynamic networks do foster cooperation. However, costs associated with dynamism such as time or resource investments in finding and establishing new partnerships have been neglected so far. Here, we show that human participants are much less likely to break links when costs arise for building new links. Especially, when costs were high, the network was nearly static. Surprisingly, cooperation levels in Prisoner's Dilemma games were not affected by reduced dynamism in social networks. We conclude that the mere
potential
to quit collaborations is sufficient in humans to reach high levels of cooperative behaviour. Effects of self-structuring processes or assortment on the network played a minor role: participants simply adjusted their cooperative behaviour in response to the threats of losing a partner or of being expelled.
Rheinheimera arenilitoris sp. nov., isolated from seashore sand
Authors: Park Sooyeon , Park Ji-Min , Won Sung-Min , Jung Yong-Taek , Yoon Jung-Hoon
Published: August 2014

A Gram-stain-negative, non-flagellated, aerobic and ovoid or rod-shaped bacterium, designated J-MS1T, was isolated from seashore sand in the South Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain J-MS1T was found to grow optimally at 30 °C and pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain J-MS1T belonged to the genus

Rheinheimera

, clustering coherently with the type strain of

Rheinheimera chironomi

and sharing 98.34 % sequence similarity. Strain J-MS1T exhibited 16S rRNA gene sequence similarity of 94.26–96.98 % to the type strains of the other species of the genus

Rheinheimera

. In the phylogenetic trees based on gyrB sequences, strain J-MS1T clustered with the type strain of

R. chironomi

, with which it shared the highest sequence similarity (86.97 %). Strain J-MS1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids detected in strain J-MS1T and in the type strain of

R. chironomi

were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain J-MS1T was 49.8 mol% and its mean DNA–DNA relatedness value with

R. chironomi

LMG 23818T was 12 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain J-MS1T is separated from recognized species of the genus

Rheinheimera

. On the basis of the data presented, strain J-MS1T is considered to represent a novel species of the genus

Rheinheimera

, for which the name Rheinheimera arenilitoris sp. nov. is proposed. The type strain is J-MS1T ( = KCTC 42112T = CECT 8623T).
Putative PmrA and PmcA are important for normal growth, morphogenesis and cell wall integrity, but not for viability in Aspergillus nidulans
Authors: Jiang Hechun , Liu Feifei , Zhang Shizhu , Lu Ling
Published: August 2014

P-type Ca2+-transporting ATPases are Ca2+pumps, extruding cytosolic Ca2+to the extracellular environment or the intracellular Ca2+store lumens. In budding yeast, Pmr1 (plasma membrane ATPase related), and Pmc1 (plasma membrane calcium-ATPase) cannot be deleted simultaneously for it to survive in standard medium. Here, we deleted two putative Ca2+pumps, designated AnPmrA and AnPmcA, fromAspergillus nidulans, and obtained the mutants ΔanpmrAand ΔanpmcA, respectively. Then, using ΔanpmrAas the starting strain, the promoter of itsanpmcAwas replaced with thealcApromoter to secure the mutant ΔanpmrAalcApmcAor itsanpmcAwas deleted completely to produce the mutant ΔanpmrAΔpmcA. Different from the case inSaccharomyces cerevisiae, double deletion ofanpmrAandanpmcAwas not lethal inA. nidulans. In addition, deletion ofanpmrAand/oranpmcAhad produced growth defects, although overexpression of AnPmc1 in ΔanpmrAalcApmcAcould not restore the growth defects that resulted from the loss of AnPmrA. Moreover, we found AnPmrA was indispensable for maintenance of normal morphogenesis, especially in low-Ca2+/Mn2+environments. Thus, our findings suggest AnPmrA and AnPmcA might play important roles in growth, morphogenesis and cell wall integrity inA. nidulansin a different way from that in yeasts.
Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString®barcode probes to specific mRNA targets
Authors: Danaher Patrick , White Robin Lynn , Hanson Erin K. , Ballantyne Jack
Published: August 2014

A DNA profile from the perpetrator does not reveal,per se, the circumstances by which it was transferred. Body fluid identification by mRNA profiling may allow extraction of contextual ‘activity level’ information from forensic samples. Here we describe the development of a prototype multiplex digital gene expression (DGE) method for forensic body fluid/tissue identification based upon solution hybridization of color-coded NanoString®probes to 23 mRNA targets. The method identifies peripheral blood, semen, saliva, vaginal secretions, menstrual blood and skin. We showed that a simple 5 minute room temperature cellular lysis protocol gave equivalent results to standard RNA isolation from the same source material, greatly enhancing the ease-of-use of this method in forensic sample processing.

We first describe a model for gene expression in a sample from a single body fluid and then extend that model to mixtures of body fluids. We then describe calculation of maximum likelihood estimates (MLEs) of body fluid quantities in a sample, and we describe the use of likelihood ratios to test for the presence of each body fluid in a sample. Known single source samples of blood, semen, vaginal secretions, menstrual blood and skin all demonstrated the expected tissue-specific gene expression for at least two of the chosen biomarkers. Saliva samples were more problematic, with their previously identified characteristic genes exhibiting poor specificity. Nonetheless the most specific saliva biomarker, HTN3, was expressed at a higher level in saliva than in any of the other tissues.

Crucially, our algorithm produced zero false positives across this study’s 89 unique samples. As a preliminary indication of the ability of the method to discern admixtures of body fluids, five mixtures were prepared. The identities of the component fluids were evident from the gene expression profiles of four of the five mixtures. Further optimization of the biomarker ‘CodeSet’ will be required before it can be used in casework, particularly with respect to increasing the signal-to-noise ratio of the saliva biomarkers. With suitable modifications, this simplified protocol with minimal hands on requirement should facilitate routine use of mRNA profiling in casework laboratories.
Dynamics of Vacuoles and H+-Pyrophosphatase Visualized by Monomeric Green Fluorescent Protein inArabidopsis: Artifactual Bulbs and Native Intravacuolar Spherical Structures
Authors: Segami Shoji , Makino Sachi , Miyake Ai , Asaoka Mariko , Maeshima Masayoshi
Published: August 2014

We prepared Arabidopsis thaliana lines expressing a functional green fluorescent protein (GFP)-linked vacuolar H+-pyrophosphatase (H+-PPase) under the control of its own promoter to investigate morphological dynamics of vacuoles and tissue-specific expression of H+-PPase. The lines obtained had spherical structures in vacuoles with strong fluorescence, which are referred to as bulbs. Quantitative analyses revealed that the occurrence of the bulbs correlated with the amount of GFP. Next, we prepared a construct of H+-PPase linked with a nondimerizing GFP (mGFP); we detected no bulbs. These results indicate that the membranes adhere face-to-face by antiparallel dimerization of GFP, resulting in the formation of bulbs. In plants expressing H+-PPase-mGFP, intravacuolar spherical structures with double membranes, which differed from bulbs in fluorescence intensity and intermembrane spacing, were still observed in peripheral endosperm, pistil epidermis and hypocotyls. Four-dimensional imaging revealed the dynamics of formation, transformation, and disappearance of intravacuolar spherical structures and transvacuolar strands in living cells. Visualization of H+-PPase-mGFP revealed intensive accumulation of the enzyme, not only in dividing and elongating cells but also in mesophyll, phloem, and nectary cells, which may have high sugar content. Dynamic morphological changes including transformation of vacuolar structures between transvacuolar strands, intravacuolar sheet-like structures, and intravacuolar spherical structures were also revealed.
Forecasting spring from afar? Timing of migration and predictability of phenology along different migration routes of an avian herbivore
Authors: Kölzsch Andrea , Bauer Silke , de Boer Rob , Griffin Larry , Cabot David , Exo Klaus‐Michael , van der Jeugd Henk P. , Nolet Bart A.
Published: August 2014

Herbivorous birds are hypothesized to migrate in spring along a seasonal gradient of plant profitability towards their breeding grounds (green wave hypothesis). For Arctic breeding species in particular, following highly profitable food is important, so that they can replenish resources along the way and arrive in optimal body condition to start breeding early.

We compared the timing of migratory movements of Arctic breeding geese on different flyways to examine whether flyways differed in the predictability of spring conditions at stopovers and whether this was reflected in the degree to which birds were following the green wave.

Barnacle geese (Branta leucopsis) were tracked with solar GPS/ARGOS PTTs from their wintering grounds to breeding sites in Greenland (N = 7), Svalbard (N = 21) and the Barents Sea (N = 12). The numerous stopover sites of all birds were combined into a set of 16 general stopover regions.

The predictability of climatic conditions along the flyways was calculated as the correlation and slope between onsets of spring at consecutive stopovers. These values differed between sites, mainly because of the presence or absence of ecological barriers. Goose arrival at stopovers was more closely tied to the local onset of spring when predictability was higher and when geese attempted breeding that year.

All birds arrived at early stopovers after the onset of spring and arrived at the breeding grounds before the onset of spring, thus overtaking the green wave. This is in accordance with patterns expected for capital breeders: first, they must come into condition; at intermediate stopovers, arrival with the food quality peak is important to stay in condition, and at the breeding grounds, early arrival is favoured so that hatching of young can coincide with the peak of food quality.

Our results suggest that a chain of correlations between climatic conditions at subsequent stopovers enables geese to closely track the green wave. However, the birds' precision of migratory timing seems uninfluenced by ecological barriers, indicating partly fixed migration schedules. These might become non‐optimal due to climate warming and preclude accurate timing of long‐distance migrants in the future.
Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments
Authors: Canion Andy , Overholt Will A. , Kostka Joel E. , Huettel Markus , Lavik Gaute , Kuypers Marcel M. M.
Published: August 2014

The temperature dependency of denitrification and anaerobic ammonium oxidation (anammox) rates from Arctic fjord sediments was investigated in a temperature gradient block incubator for temperatures ranging from −1 to 40°C. Community structure in intact sediments and slurry incubations was determined using Illumina SSU rRNA gene sequencing. The optimal temperature (Topt) for denitrification was 25–27°C, whereas anammox rates were optimal at 12–17°C. Both denitrification and anammox exhibited temperature responses consistent with a psychrophilic community, but anammox bacteria may be more specialized for psychrophilic activity. Long‐term (1–2 months) warming experiments indicated that temperature increases of 5–10°C above in situ had little effect on the microbial community structure or the temperature response of denitrification and anammox. Increases of 25°C shifted denitrification temperature responses to mesophilic with concurrent community shifts, and anammox activity was eliminated above 25°C. Additions of low molecular weight organic substrates (acetate and lactate) caused increases in denitrification rates, corroborating the hypothesis that the supply of organic substrates is a more dominant control of respiration rates than low temperature. These results suggest that climate‐related changes in sinking particulate flux will likely alter rates of N removal more rapidly than warming.