bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept
Authors: Herrera Carlos M. , Medrano Mónica , Bazaga Pilar 
Published: February 2016

AbstractDespite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation‐by‐distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity‐distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation‐sensitive AFLP markers. Expectations from individual‐level IBD patterns were tested by means of kinship‐distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual‐level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic ‘kinship excess’ tending to decrease as plant separation increased. Results suggest that moderate‐to‐high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
Development and evaluation of real‐time PCR assays for bloodmeal identification in Culicoides midges
Authors: VAN DER SAAG M. R. , GU X. , WARD M. P. , KIRKLAND P. D. 
Published: February 2016

AbstractCulicoides (Diptera: Ceratopogonidae) midges are the biological vectors of a number of arboviruses of veterinary importance. However, knowledge relating to the basic biology of some species, including their host‐feeding preferences, is limited. Identification of host‐feeding preferences in haematophagous insects can help to elucidate the transmission dynamics of the arboviruses they may transmit. In this study, a series of semi‐quantitative real‐time polymerase chain reaction (qPCR) assays to identify the vertebrate host sources of bloodmeals of Culicoides midges was developed. Two pan‐reactive species group and seven species‐specific qPCR assays were developed and evaluated. The assays are quick to perform and less expensive than nucleic acid sequencing of bloodmeals. Using these assays, it was possible to rapidly test nearly 700 blood‐fed midges of various species from several geographic locations in Australia.
When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts inVenturia inaequalis
Authors: Leroy Thibault , Caffier Valérie , Celton Jean‐Marc , Anger Nicolas , Durel Charles‐Eric , Lemaire Christophe , Le Cam Bruno 
Published: February 2016

SummaryIn pathogens, introgressions through secondary contacts between divergent populations from agricultural and nonagricultural disease reservoirs are expected to have crucial evolutionary and epidemiological implications. Despite the importance of this question for disease management, experimental demonstrations of these implications remain scarce.Recently, we identified a virulent population of the apple scab pathogenVenturia inaequalisthat migrated from nonagricultural hosts to European domestic apple orchards. Here, we investigated the occurrence of gene flow between agricultural and nonagricultural populations sampled in two orchards, and thereafter its consequences on the pathogenicity of hybrids.Population genetic structure and demographic inferences based on the genotypes of 104 strains revealed a high amount of gene flow between the two populations in one orchard. In this site, mating between populations was made possible by the presence of a common host. Our results revealed an invasion of the virulent trait in the agricultural population; a main direction of introgression in hybrids from the agricultural to nonagricultural genetic backgrounds; and a population of hybrids with transgressive traits.We demonstrate a secondary contact with gene flow between divergent populations of pathogens. Our findings highlight evolutionary and epidemiological changes in pathogens and have concrete implications for sustainable disease management.
Enhancing the evaluation of PI3K inhibitors through 3D melanoma models
Authors: Shannan Batool , Chen Quan , Watters Andrea , Perego Michela , Krepler Clemens , Thombre Rakhee , Li Ling , Rajan Geena , Peterson Scott , Gimotty Phyllis A. , Wilson Melissa , Nathanson Katherine L. , Gangadhar Tara C. , Schuchter Lynn M. , Weeraratna Ashani T. , Herlyn Meenhard , Vultur Adina 
Published: February 2016

SummaryTargeted therapies for mutant BRAF metastatic melanoma are effective but not curative due to acquisition of resistance. PI3K signaling is a common mediator of therapy resistance in melanoma; thus, the need for effective PI3K inhibitors is critical. However, testing PI3K inhibitors in adherent cultures is not always reflective of their potential in vivo. To emphasize this, we compared PI3K inhibitors of different specificity in two‐ and three‐dimensional (2D, 3D) melanoma models and show that drug response predictions gain from evaluation using 3D models. Our results in 3D demonstrate the anti‐invasive potential of PI3K inhibitors and that drugs such as PX‐866 have beneficial activity in physiological models alone and when combined with BRAF inhibition. These assays finally help highlight pathway effectors that could be involved in drug response in different environments (e.g. p4E‐BP1). Our findings show the advantages of 3D melanoma models to enhance our understanding of PI3K inhibitors.
Epidemiological Evidence for a Decreasing Incidence of Neonatal Abstinence Syndrome, 2000–11
Authors: Uebel Hannah , Wright Ian M. , Burns Lucy , Hilder Lisa , Bajuk Barbara , Breen Courtney , Abdel‐Latif Mohamed E. , Ward Meredith , Eastwood John , Feller John M. , Falconer Janet , Clews Sara , Oei Ju Lee 
Published: February 2016

AbstractBackgroundThis study analyses the incidence of Neonatal Abstinence Syndrome (NAS) in a large geographically defined population in Australia.MethodDatabase linkage analysis of all births between 2000 and 2011 in New South Wales (NSW), Australia. The diagnosis of NAS was derived from hospital coding P96.1, ‘Neonatal withdrawal symptoms from maternal use of drugs of addiction’. Temporal trends were studied by comparing epoch 1 (2000–05) with epoch 2 (2006–11). The relationship with changes in maternal factors was further analysed.ResultsThe NAS was coded in 3842 of 1 022 263 live born infants (0.38%). NAS incidence peaked at 5.07 per 1000 live births in 2002, decreasing to 3.18 in 2011 and was negatively correlated with maternal age (r = −0.7). The rate of NAS in epoch 2 (3.4 per 1000 births, 95% CI 3.28, 3.58) was significantly lower than in epoch 1 (4.1 per 1000 births, 95% CI 3.96, 4.33). Epoch 2 mothers were significantly older (mean 29.8 years vs. 28.3 years), less likely to be multiparous (OR 0.7, 95% CI 0.6, 0.9) or smoke (OR 0.4, 95% CI 0.4, 0.5). They were more likely to engage in antenatal care earlier (mean first visit: 14.1 vs. 18.9 weeks). Most infants (~80%) were born at term (>37 weeks gestation).ConclusionThe incidence of NAS as a discharge diagnosis has decreased in our population since 2002. Mothers are also older and engaging earlier in prenatal care. Whether these changes alter NAS presentation and diagnosis or whether pregnant women are using drugs that do not cause typical NAS (e.g. amphetamines) is uncertain and requires further study.
Regulatory Transformation: Lessons from Connecticut's Department of Energy and Environmental Protection
Authors: Esty Daniel 
Published: February 2016

AbstractAs economies and citizen priorities continue to evolve, governance practices must also adjust to changing circumstances and public expectations. This article explores the important topic of regulatory transformation, drawing from both the academic literature and the author's recent experience heading Connecticut's Department of Energy and Environmental Protection. The article makes the case for a focus on vision and execution as the critical starting points for good governance in the twenty‐first century, drawing on best practices from the world of management. It then addresses some of the constraints faced by government organizations in this evolving era. Finally, the article identifies five core elements of regulatory excellence: integration, innovation, incentives, investment, and implementation.
Taylor's Power Law and the Statistical Modelling of Infectious Disease Surveillance Data
Authors: Enki Doyo Gragn , Noufaily Angela , Farrington Paddy , Garthwaite Paul , Andrews Nick , Charlett Andre 
Published: February 2016

Summary
Surveillance data collected on several hundred different infectious organisms over 20 years have revealed striking power relationships between their variance and mean in successive time periods. Such patterns are common in ecology, where they are referred to collectively as Taylor's power law. In the paper, these relationships are investigated in detail, with the aim of exploiting them for the descriptive statistical modelling of infectious disease surveillance data. We confirm the existence of variance-to-mean power relationships, with exponent typically between 1 and 2. We investigate skewness-to-mean relationships, which are found broadly to match those expected of Tweedie distributions, and thus confirm the relevance of the Tweedie convergence theorem in this context. We suggest that variance- and skewness-to-mean power laws, when present, should inform statistical modelling of infectious disease surveillance data, notably in descriptive analysis, model building, simulation and interval and threshold estimation, threshold estimation being particularly relevant to outbreak detection.
Identifying Subgroups of Enhanced Predictive Accuracy from Longitudinal Biomarker Data by Using Tree-Based Approaches: Applications to Fetal Growth
Authors: Foster Jared C. , Liu Danping , Albert Paul S. , Liu Aiyi 
Published: February 2016

Summary
Longitudinal monitoring of biomarkers is often helpful for predicting disease or a poor clinical outcome. We consider the prediction of both large and small for gestational age births by using longitudinal ultrasound measurements, and we attempt to identify subgroups of women for whom prediction is more (or less) accurate, should they exist. We propose a tree-based approach to identifying such subgroups, and a pruning algorithm which explicitly incorporates a desired type I error rate, allowing us to control the risk of false discovery of subgroups. The methods proposed are applied to data from the Scandinavian Fetal Growth Study and are evaluated via simulations.
Assessing the Inequality of Lifetime Healthcare Expenditures: a Nearest Neighbour Resampling Approach
Authors: Wong Albert , Boshuizen Hendriek , Polder Johan , Ferreira José António 
Published: February 2016

SummaryThe rise in healthcare expenditures has raised doubts about the sustainability of health systems and instigated a discussion on their design. Policy making in this field requires a proper understanding of how healthcare expenditures evolve throughout an individual's lifetime, and of how they vary between individuals. Given the lack of data on healthcare expenditures during an individual's lifetime, we developed a new nearest neighbour resampling approach to construct realistic individual life cycles of healthcare expenditures based on cross-sectional data from the Netherlands. This approach provides insight into lifetime healthcare expenditures. Our main finding is that the inequality in lifetime healthcare expenditures is much smaller than the inequality as derived from cross-sectional healthcare expenditures.
A TILLING approach to generate broad‐spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy
Authors: Gauffier Camille , Lebaron Caroline , Moretti André , Constant Carole , Moquet Frédéric , Bonnet Grégori , Caranta Carole , Gallois Jean‐Luc 
Published: February 2016

SummaryGenetic resistance to pathogens is important for sustainable maintenance of crop yields. Recent biotechnologies offer alternative approaches to generate resistant plants by compensating for the lack of natural resistance. Tomato (Solanum lycopersicum) and related species offer a model in which natural and TILLING‐induced potyvirus resistance alleles may be compared. For resistance based on translation initiation factor eIF4E1, we confirm that the natural allele Sh–eIF4E1PI24–pot1, isolated from the wild tomato species Solanum habrochaites, is associated with a wide spectrum of resistance to both potato virus Y and tobacco etch virus isolates. In contrast, a null allele of the same gene, isolated through a TILLING strategy in cultivated tomato S. lycopersicum, is associated with a much narrower resistance spectrum. Introgressing the null allele into S. habrochaites did not extend its resistance spectrum, indicating that the genetic background is not responsible for the broad resistance. Instead, the different types of eIF4E1 mutations affect the levels of eIF4E2 differently, suggesting that eIF4E2 is also involved in potyvirus resistance. Indeed, combining two null mutations affecting eIF4E1 and eIF4E2 re‐establishes a wide resistance spectrum in cultivated tomato, but to the detriment of plant development. These results highlight redundancy effects within the eIF4E gene family, where regulation of expression alters susceptibility or resistance to potyviruses. For crop improvement, using loss‐of‐function alleles to generate resistance may be counter‐productive if they narrow the resistance spectrum and limit growth. It may be more effective to use alleles encoding functional variants similar to those found in natural diversity.
Metabolic Engineering of Probiotic Saccharomyces boulardii
Authors: Liu Jing-Jing , Kong In Iok , Zhang Guo-Chang , Jayakody Lahiru N. , Kim Heejin , Xia Peng-Fei , Kwak Suryang , Sung Bong Hyun , Sohn Jung-Hoon , Walukiewicz Hanna E. , Rao Christopher V. , Jin Yong-Su 
Published: February 2016

ABSTRACT

Saccharomyces boulardii
is a probiotic yeast that has been used for promoting gut health as well as preventing diarrheal diseases. This yeast not only exhibits beneficial phenotypes for gut health but also can stay longer in the gut than
Saccharomyces cerevisiae
. Therefore,
S. boulardii
is an attractive host for metabolic engineering to produce biomolecules of interest in the gut. However, the lack of auxotrophic strains with defined genetic backgrounds has hampered the use of this strain for metabolic engineering. Here, we report the development of well-defined auxotrophic mutants (
leu2
,
ura3
,
his3
, and
trp1
) through clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-based genome editing. The resulting auxotrophic mutants can be used as a host for introducing various genetic perturbations, such as overexpression or deletion of a target gene, using existing genetic tools for
S. cerevisiae
. We demonstrated the overexpression of a heterologous gene (
lacZ
), the correct localization of a target protein (red fluorescent protein) into mitochondria by using a protein localization signal, and the introduction of a heterologous metabolic pathway (xylose-assimilating pathway) in the genome of
S. boulardii
. We further demonstrated that human lysozyme, which is beneficial for human gut health, could be secreted by
S. boulardii
. Our results suggest that more sophisticated genetic perturbations to improve
S. boulardii
can be performed without using a drug resistance marker, which is a prerequisite for
in vivo
applications using engineered
S. boulardii
.
CO Metabolism in the Thermophilic Acetogen Thermoanaerobacter kivui
Authors: Weghoff Marie Charlotte , Müller Volker 
Published: February 2016

ABSTRACT

The thermophilic acetogenic bacterium
Thermoanaerobacter kivui
, previously described not to use carbon monoxide as a carbon and energy source, was adapted to grow on CO. This was achieved by using a preculture grown on H
2
plus CO
2
and by increasing the CO concentration in small, 10% increments.
T. kivui
was finally able to grow within a 100% CO atmosphere. Growth on CO was found in complex and mineral media, and vitamins were not required. Carbon monoxide consumption was accompanied by acetate and hydrogen production. Cells also grew on synthesis gas (syngas) with the simultaneous use of CO and H
2
coupled to acetate production. CO oxidation in resting cells was coupled to hydrogen and acetate production and accompanied by the synthesis of ATP. A protonophore abolished ATP synthesis but stimulated H
2
production, which is consistent with a chemiosmotic mechanism of ATP synthesis. Hydrogenase activity was highest in crude extracts of CO-grown cells, and carbon monoxide dehydrogenase (CODH) activity was highest in H
2
-plus-CO
2
- or CO-grown cells. The genome of
T. kivui
harbors two CODH gene clusters, and both CODH proteins were present in crude extracts, but one CODH was more prevalent in crude extracts from CO-grown cells.
Ultrastructural Variability of the Exosporium Layer of Clostridium difficile Spores
Authors: Pizarro-Guajardo Marjorie , Calderón-Romero Paulina , Castro-Córdova Pablo , Mora-Uribe Paola , Paredes-Sabja Daniel 
Published: February 2016

ABSTRACT

The anaerobic sporeformer
Clostridium difficile
is the leading cause of nosocomial antibiotic-associated diarrhea in developed and developing countries. The metabolically dormant spore form is considered the transmission, infectious, and persistent morphotype, and the outermost exosporium layer is likely to play a major role in spore-host interactions during the first contact of
C. difficile
spores with the host and for spore persistence during recurrent episodes of infection. Although some studies on the biology of the exosporium have been conducted (J. Barra-Carrasco et al., J Bacteriol 195:3863–3875, 2013,
http://dx.doi.org/10.1128/JB.00369-13
; J. Phetcharaburanin et al., Mol Microbiol 92:1025–1038, 2014,
http://dx.doi.org/10.1111/mmi.12611
), there is a lack of information on the ultrastructural variability and stability of this layer. In this work, using transmission electron micrographs, we analyzed the variability of the spore's outermost layers in various strains and found distinctive variability in the ultrastructural morphotype of the exosporium within and between strains. Through transmission electron micrographs, we observed that although this layer was stable during spore purification, it was partially lost after 6 months of storage at room temperature. These observations were confirmed by indirect immunofluorescence microscopy, where a significant decrease in the levels of two exosporium markers, the N-terminal domain of BclA1 and CdeC, was observed. It is also noteworthy that the presence of the exosporium marker CdeC on spores obtained from
C. difficile
biofilms depended on the biofilm culture conditions and the strain used. Collectively, these results provide information on the heterogeneity and stability of the exosporium surface of
C. difficile
spores. These findings have direct implications and should be considered in the development of novel methods to diagnose and/or remove
C. difficile
spores by using exosporium proteins as targets.
Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress
Authors: Lima-Morales Daiana , Jáuregui Ruy , Camarinha-Silva Amelia , Geffers Robert , Pieper Dietmar H. , Vilchez-Vargas Ramiro 
Published: February 2016

ABSTRACT

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive
in situ
bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.
New Recombinant Mycobacterium bovis BCG Expression Vectors: Improving Genetic Control over Mycobacterial Promoters
Authors: Kanno Alex I. , Goulart Cibelly , Rofatto Henrique K. , Oliveira Sergio C. , Leite Luciana C. C. , McFadden Johnjoe 
Published: February 2016

ABSTRACT

The expression of many antigens, stimulatory molecules, or even metabolic pathways in mycobacteria such as
Mycobacterium bovis
BCG or
M. smegmatis
was made possible through the development of shuttle vectors, and several recombinant vaccines have been constructed. However, gene expression in any of these systems relied mostly on the selection of natural promoters expected to provide the required level of expression by trial and error. To establish a systematic selection of promoters with a range of strengths, we generated a library of mutagenized promoters through error-prone PCR of the strong P
L5
promoter, originally from mycobacteriophage L5. These promoters were cloned upstream of the enhanced green fluorescent protein reporter gene, and recombinant
M. smegmatis
bacteria exhibiting a wide range of fluorescence levels were identified. A set of promoters was selected and identified as having high (pJK-F8), intermediate (pJK-B7, pJK-E6, pJK-D6), or low (pJK-C1) promoter strengths in both
M. smegmatis
and
M. bovis
BCG. The sequencing of the promoter region demonstrated that it was extensively modified (6 to 11%) in all of the plasmids selected. To test the functionality of the system, two different expression vectors were demonstrated to allow corresponding expression levels of the
Schistosoma mansoni
antigen Sm29 in BCG. The approach used here can be used to adjust expression levels for synthetic and/or systems biology studies or for vaccine development to maximize the immune response.