bluuebunny/crossref_metadata_2025 huggingface dataset:
Buchnera has changed flatmate but the repeated replacement of co‐obligate symbionts is not associated with the ecological expansions of their aphid hosts
Authors: Meseguer A. S. , Manzano‐Marín A. , Coeur d'Acier A. , Clamens A.‐L. , Godefroid M. , Jousselin E.
Published: November 2016

Symbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long‐term obligate interactions. Recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement, and/or supplementation of an obligate symbiosis by an additional bacterium, has occurred during the history of many insect groups. Yet, the factors favouring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a ‘ménage à trois’, in which Buchnera is complemented by a cosymbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species confirm that these coresident symbionts fulfil essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that cosymbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.
Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations
Authors: Mohd‐Assaad Norfarhan , McDonald Bruce A. , Croll Daniel
Published: November 2016

Evolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene (CYP51) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CYP51 mutations and the mechanisms leading to CYP51‐independent resistance are poorly understood. We used whole‐genome sequencing and genome‐wide association studies (GWAS) to perform an unbiased screen of azole resistance loci in Rhynchosporium commune, the causal agent of the barley scald disease. We assayed cyproconazole resistance in 120 isolates collected from nine populations worldwide. We found that mutations in highly conserved genes encoding the vacuolar cation channel YVC1, a transcription activator, and a saccharopine dehydrogenase made significant contributions to fungicide resistance. These three genes were not previously known to confer resistance in plant pathogens. However, YVC1 is involved in a conserved stress response pathway known to respond to azoles in human pathogenic fungi. We also performed GWAS to identify genetic polymorphism linked to fungal growth rates. We found that loci conferring increased fungicide resistance were negatively impacting growth rates, suggesting that fungicide resistance evolution imposed costs. Analyses of population structure showed that resistance mutations were likely introduced into local populations through gene flow. Multilocus resistance evolution to fungicides shows how pathogen populations can evolve a complex genetic architecture for an important phenotypic trait within a short time span.
PrgU: a suppressor of sex pheromone toxicity in Enterococcus faecalis
Authors: Bhatty Minny , Camacho Martha I. , Gonzalez‐Rivera Christian , Frank Kristi L. , Dale Jennifer L. , Manias Dawn A. , Dunny Gary M. , Christie Peter J.
Published: November 2016

Upon sensing of the peptide pheromone cCF10, Enterococcus faecalis cells carrying pCF10 produce three surface adhesins (PrgA, PrgB or Aggregation Substance, PrgC) and the Prg/Pcf type IV secretion system and, in turn, conjugatively transfer the plasmid at high frequencies to recipient cells. Here, we report that cCF10 induction is highly toxic to cells sustaining a deletion of prgU, a small orf located immediately downstream of prgB on pCF10. Upon pheromone exposure, these cells overproduce the Prg adhesins and display impaired envelope integrity, as evidenced by antibiotic susceptibility, misplaced division septa and cell lysis. Compensatory mutations in regulatory loci controlling expression of pCF10‐encoded prg/pcf genes, or constitutive PrgU overproduction, block production of the Prg adhesins and render cells insensitive to pheromone. Cells engineered to overproduce PrgB, even independently of other pCF10‐encoded proteins, have severely compromised cell envelopes and strong growth defects. PrgU has an RNA‐binding fold, and prgB‐prgU gene pairs are widely distributed among E. faecalis isolates and other enterococcal and staphylococcal species. Together, our findings support a model in which PrgU proteins represent a novel class of RNA‐binding regulators that act to mitigate toxicity accompanying overproduction of PrgB‐like adhesins in E. faecalis and other clinically‐important Gram‐positive species.
Discovery of the type VII ESX‐1 secretion needle?
Authors: Ates Louis S. , Brosch Roland
Published: November 2016

Mycobacterium tuberculosis, the etiological agent of human tuberculosis, harbours five ESAT‐6/type VII secretion (ESX/T7S) systems. The first esx gene clusters were identified during the genome‐sequencing project of M. tuberculosis H37Rv. Follow‐up studies revealed additional genes playing important roles in ESX/T7S systems. Among the latter genes, one can find those that encode Pro‐Glu (PE) and Pro‐Pro‐Glu (PPE) proteins as well as a gene cluster that is encoded >260 kb upstream of the esx‐1 locus and encodes ESX‐1 secretion‐associated proteins EspA (Rv3616c), EspC (Rv3615c) and EspD (Rv3614c). The espACD cluster has been suggested to have an important function in ESX‐1 secretion since EspA‐EspC and EsxA–EsxB are mutually co‐dependent on each other for secretion. However, the molecular mechanism of this co‐dependence and interaction between the substrates remained unknown. In this issue of Molecular Microbiology, Lou and colleagues show that EspC forms high‐molecular weight polymerization complexes that resemble selected components of type II, III and/or IV secretion systems of Gram‐negative bacteria. Indeed, EspC‐multimeric complexes form filamentous structures that could well represent a secretion needle of ESX‐1 type VII secretion systems. This exciting observation opens new avenues for research to discover and characterize ESX/T7S components and elucidates the co‐dependence of EsxA/B secretion with EspA/C.
Reason After Revelation: Karl Barth on Divine Word and Human Words
Authors: Woodard‐Lehman Derek Alan
Published: November 2016

Though little understood, Karl Barth's moral theology is widely criticized. Indeed, it is so widely criticized because it is so little understood. Among ethicists, the principal objects of criticism are Barth's account of practical reason and the account of revelation on which it depends. This essay argues that such criticisms miss their mark, because they rest on an incomplete understanding of Barth's doctrine of the Word of God that results in an incorrect understanding of his doctrine of divine command. Because critics neglect his account of subjective reception of revelation through which divine command is heard, they ignore the account of disputation, deliberation, and decision present in his account of scriptural interpretation and ecclesial confession. By laying out the discursive practices of scriptural interpretation and ecclesial confession, and by drawing out the deliberative dimensions of Kantian self‐legislation and Hegelian mutual recognition at work in interpretation and confession alike, this essay argues that these practices provide a fuller account of what Barth calls “practical casuistry,” as well as his most fulsome and winsome account of practical reason.
Transcriptional response of Erwinia amylovora to copper shock: in vivo role of the copA gene
Authors: Águila‐Clares Begoña , Castiblanco Luisa F. , Quesada José Miguel , Penyalver Ramón , Carbonell Juan , López María M. , Marco‐Noales Ester , Sundin George W.
Published: November 2016

Fire blight is a devastating plant disease caused by the bacterium Erwinia amylovora, and its control is frequently based on the use of copper‐based compounds whose mechanisms of action are not well known. Consequently, in this article, we investigate the response of E. amylovora to copper shock by a whole‐genome microarray approach. Transcriptional analyses showed that, in the presence of copper, 23 genes were increased in expression; these genes were classified mainly into the transport and stress functional categories. Among them, the copA gene was strongly induced and regulated in a finely tuned manner by copper. Mutation of copA, soxS, arcB, yjcE, ygcF, yhhQ, galF and EAM_3469 genes revealed that tolerance to copper in E. amylovora can be achieved by complex physiological mechanisms, including: (i) the control of copper homeostasis through, at least, the extrusion of Cu(I) by a P‐type ATPase efflux pump CopA; and (ii) the overcoming of copper toxicity caused by oxidative stress by the expression of several reactive oxygen species (ROS)‐related genes, including the two major transcriptional factors SoxS and ArcB. Furthermore, complementation analyses demonstrated the important role of copA for copper tolerance in E. amylovora, not only in vitro, but also in inoculated pear shoots.
Comparative evaluation of pan‐fungal real‐time PCR, galactomannan and (1‐3)‐β‐D‐glucan assay for invasive fungal infection in paediatric cancer patients
Authors: Gupta Prashant , Ahmad Abrar , Khare Vineeta , Kumar Archana , Banerjee Gopa , Verma Nitya , Singh Mastan
Published: November 2016

Limited specific data and investigations are available for the diagnosis of Invasive Fungal Infection (IFI) in paediatrics cancer patients. Three non‐invasive tests; Platelia Aspergillus EIA for galactomannan (GM), β‐D‐glucan (BDG) assay and pan‐fungal real‐time PCR for fungal DNA in blood were evaluated. One hundred twenty‐five paediatrics cancer patients at the high risk of IFI were enrolled. Single blood and serum samples were evaluated by all the three methods. Patients were classified into 10 proven, 52 probable and 63 no IFI cases in accordance with EORTC MSG 2008 revised guidelines. The sensitivity, specificity, PPV and NPV of all the three tests in proven, probable and no IFIs cases were analysed singly and in combination. The sensitivity, specificity, PPV and NPV of GM, BDG and pan‐fungal real‐time PCR were: 87%, 61%, 81%, 69.5% for GM, 88%, 59.5%, 81%, 71.4% for BDG and 89%, 69.2%, 85%, 67.5% for PCR (95% CI). Among different combinations, best combination was found to be GM and PCR with sensitivity, specificity, PPV and NPV of 98.2%, 89.3%, 97.1% and 90% respectively. Single samples must be evaluated by combination of tests.
An update of the evidence relating to plant‐based diets and cardiovascular disease, type 2 diabetes and overweight
Authors: Harland J. , Garton L.
Published: November 2016

Recent findings from meta‐analyses, European cohorts and randomised controlled trials (RCTs) evaluating the relationship between plant‐based dietary regimes (i.e. those with an emphasis on plant foods, such as vegetarian, vegan, Mediterranean or combination diets), and the incidence of, or risk factors for, cardiovascular disease (CVD), type 2 diabetes (T2D) and obesity are considered in this review. Evidence from meta‐analyses of epidemiological studies indicates that those following plant‐based dietary regimes have around 20–25% lower risk of developing CVD and a similar reduced risk of developing T2D. Evidence from RCTs indicates that those following plant‐based dietary regimes have lower total cholesterol, low‐density lipoprotein‐cholesterol and blood pressure, and modest reductions in inflammatory and endothelial markers. Higher intake of plant foods has been associated with lower incidence of obesity, lower BMI and smaller waist circumference. For weight loss, it seems that following a plant‐based dietary regime results in weight loss comparable to that achieved on conventional reduced calorie diets, but with better overall weight management. The totality of evidence indicates there are benefits for cardiovascular health, risk of developing T2D and weight management from following a plant‐based dietary regime. From a nutritional perspective, plant‐based diets tend to be lower in saturated fatty acids, higher in unsaturated fatty acids and fibre, and lower in energy density than typical ‘Western’ diets. These qualities may be at the core of the health benefits reported and/or it may be simply a greater proportion of plant foods in the diet that is beneficial in its own right.
Personalised nutrition: What makes you so special?
Authors: Betts J. A. , Gonzalez J. T.
Published: November 2016

Personalised nutrition can be defined as developing unique nutrition guidelines for each individual; precision nutrition seeks to develop effective approaches based on the combination of an individual's genetic, environmental and lifestyle factors. The former infers variants that underlie traits are largely fixed (i.e. stable across time) and appeals to the notion that we are inherently different from one another. The latter opens up the possibility that what we do and where we are may be more important than what we are. While there are undoubtedly a specific minority of individuals who clearly require a more personalised approach to nutrition, several criteria must be fulfilled before we can justify or implement personalised nutrition for the general population. These would include identifying a desired health outcome and a valid predictor of how that outcome changes, which can be measured with sufficient accuracy and exhibit a robust correlation and/or causal relationship in the required direction (i.e. predictor‐response). Many attempts to personalise nutrition, such as profiling the genome or microbiome, do not currently meet all these criteria. Therefore, we argue that there is presently insufficient rationale for truly personalised nutrition for the majority of people based on the inter‐individual differences that separate them. Conversely, we propose that precision nutrition based on the environmental and/or behavioural ‘lifestyle’ variance within each person may provide a more effective basis for adjusting diet dynamically, with recognition of varying physiological demands and requirements over time.
Guidance for the design and implementation of human dietary intervention studies for health claim submissions
Authors: Lucey A. , Heneghan C. , Kiely M. E.
Published: November 2016

The recently completedEU‐fundedBACCHUSIntegrated Project (grant number: 312090) has focused on identification of cause‐and‐effect relationships between consumption of bioactive peptides and polyphenols and physiological effects on cardiovascular health. An importantBACCHUSoutput is a toolkit to support the needs of small‐ and medium‐sized enterprises (SMEs) in the food sector considering making health claims on their products. The toolkit draws together best practice guides, a bioactives database, an intake assessment tool and an e‐learning platform. This paper focuses on theBest Practice Guide for Human Dietary Intervention Studies. The toolkit has been developed withSMEs in mind but this guidance is likely to have value far beyond the needs of businesses, in particular being a useful resource for students, early‐career scientists and others new to the design and implementation of dietary intervention studies. The aim of this article is to share the principles of the guide with a broader audience.
Arabidopsis thaliana FAR‐RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR‐RED‐IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar
Authors: Ma Lin , Xue Na , Fu Xiaoyu , Zhang Haisen , Li Gang
Published: November 2016

In living organisms, daily light/dark cycles profoundly affect cellular processes. In plants, optimal growth and development, and adaptation to daily light–dark cycles, require starch synthesis and turnover. However, the underlying molecular mechanisms coordinating daily starch metabolism remain poorly understood.

To explore the roles of Arabidopsis thaliana light signal transduction proteins FAR‐RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR‐RED‐IMPAIRED RESPONSE1 (FAR1) in starch metabolism, the contents of starch and water‐soluble polysaccharides, and the structure of starch granules were investigated in fhy3, far1 and fhy3 far1 mutant plants.

Disruption of FHY3 or FAR1 reduced starch accumulation and altered starch granule structure in the fhy3‐4, far1‐2, and fhy3‐4 far1‐2 mutant plants. Furthermore, molecular and genetic evidence revealed that the gene encoding the starch‐debranching enzyme ISOAMYLASE2 (ISA2) is a direct target of FHY3 and FAR1, and functions in light‐induced starch synthesis.

Our data establish the first molecular link between light signal transduction and starch synthesis, suggesting that the light‐signaling proteins FHY3 and FAR1 influence starch synthesis and starch granule formation through transcriptional activation of ISA2.
Respiration climacteric in tomato fruits elucidated by constraint‐based modelling
Authors: Colombié Sophie , Beauvoit Bertrand , Nazaret Christine , Bénard Camille , Vercambre Gilles , Le Gall Sophie , Biais Benoit , Cabasson Cécile , Maucourt Mickaël , Bernillon Stéphane , Moing Annick , Dieuaide‐Noubhani Martine , Mazat Jean‐Pierre , Gibon Yves
Published: November 2016

Tomato is a model organism to study the development of fleshy fruit including ripening initiation. Unfortunately, few studies deal with the brief phase of accelerated ripening associated with the respiration climacteric because of practical problems involved in measuring fruit respiration.

Because constraint‐based modelling allows predicting accurate metabolic fluxes, we investigated the respiration and energy dissipation of fruit pericarp at the breaker stage using a detailed stoichiometric model of the respiratory pathway, including alternative oxidase and uncoupling proteins. Assuming steady‐state, a metabolic dataset was transformed into constraints to solve the model on a daily basis throughout tomato fruit development.

We detected a peak of CO2 released and an excess of energy dissipated at 40 d post anthesis (DPA) just before the onset of ripening coinciding with the respiration climacteric. We demonstrated the unbalanced carbon allocation with the sharp slowdown of accumulation (for syntheses and storage) and the beginning of the degradation of starch and cell wall polysaccharides. Experiments with fruits harvested from plants cultivated under stress conditions confirmed the concept.

We conclude that modelling with an accurate metabolic dataset is an efficient tool to bypass the difficulty of measuring fruit respiration and to elucidate the underlying mechanisms of ripening.
A core function of EDS1 with PAD4 is to protect the salicylic acid defense sector in Arabidopsis immunity
Authors: Cui Haitao , Gobbato Enrico , Kracher Barbara , Qiu Jingde , Bautor Jaqueline , Parker Jane E.
Published: November 2016

Plant defenses induced by salicylic acid (SA) are vital for resistance against biotrophic pathogens. In basal and receptor‐triggered immunity, SA accumulation is promoted by Enhanced Disease Susceptibility1 with its co‐regulator Phytoalexin Deficient4 (EDS1/PAD4). Current models position EDS1/PAD4 upstream of SA but their functional relationship remains unclear.

In a genetic and transcriptomic analysis of Arabidopsis autoimmunity caused by constitutive or conditional EDS1/PAD4 overexpression, intrinsic EDS1/PAD4 signaling properties and their relation to SA were uncovered.

A core EDS1/PAD4 pathway works in parallel with SA in basal and effector‐triggered bacterial immunity. It protects against disabled SA‐regulated gene expression and pathogen resistance, and is distinct from a known SA‐compensatory route involving MAPK signaling. Results help to explain previously identified EDS1/PAD4 regulated SA‐dependent and SA‐independent gene expression sectors.

Plants have evolved an alternative route for preserving SA‐regulated defenses against pathogen or genetic perturbations. In a proposed signaling framework, EDS1 with PAD4, besides promoting SA biosynthesis, maintains important SA‐related resistance programs, thereby increasing robustness of the innate immune system.
A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin
Authors: da Costa Ricardo M. F. , Pattathil Sivakumar , Avci Utku , Lee Scott J. , Hazen Samuel P. , Winters Ana , Hahn Michael G. , Bosch Maurice
Published: November 2016

Miscanthus spp. are promising lignocellulosic energy crops, but cell wall recalcitrance to deconstruction still hinders their widespread use as bioenergy and biomaterial feedstocks. Identification of cell wall characteristics desirable for biorefining applications is crucial for lignocellulosic biomass improvement. However, the task of scoring biomass quality is often complicated by the lack of a reference for a given feedstock.

A multidimensional cell wall analysis was performed to generate a reference profile for leaf and stem biomass from several miscanthus genotypes harvested at three developmentally distinct time points. A comprehensive suite of 155 monoclonal antibodies was used to monitor changes in distribution, structure and extractability of noncellulosic cell wall matrix glycans.

Glycan microarrays complemented with immunohistochemistry elucidated the nature of compositional variation, and in situ distribution of carbohydrate epitopes. Key observations demonstrated that there are crucial differences in miscanthus cell wall glycomes, which may impact biomass amenability to deconstruction.

For the first time, variations in miscanthus cell wall glycan components were comprehensively characterized across different harvests, organs and genotypes, to generate a representative reference profile for miscanthus cell wall biomass. Ultimately, this portrait of the miscanthus cell wall will help to steer breeding and genetic engineering strategies for the development of superior energy crops.
Colony and evolutionary dynamics of a two‐stage model with brood cannibalism and division of labor in social insects
Authors: Rodriguez‐Rodriguez Marisabel , Kang Yun
Published: November 2016

Division of labor (DOL) is a major factor for the great success of social insects because it increases the efficiency of a social group where different individuals perform different tasks repeatedly and presumably with increased performance. Cannibalism plays an important role in regulating colony growth and development by regulating the number of individuals in a colony and increasing survival by providing access to essential nutrients and minimizing competition among colony mates. To understand the synergy effects of DOL and cannibalistic behavior on colony dynamic outcomes, we propose and study a compartmental two‐stage model using ecological and evolutionary game theory settings. Our analytical results of the ecological and evolutionary models suggest that: (1) A noncannibalistic colony can survive if the efficiency of energy investment reflecting the DOL is greater than the relative death rate of the older population. (2) A cannibalistic colony can die out if both the efficiency of energy investment and the relative cannibalism rate (where each is also reflecting the DOL) are too large; or if the relative cannibalism rate alone is too small. (3) From our numerical analysis, cannibalism can increase or reduce the colony's total population size, which greatly depends on the benefit of egg cannibalism increasing or decreasing of adult's lifespan. (4) A cannibalistic and noncannibalistic colony can experience bistability due to cooperative behavior. (5) In the evolutionary settings, DOL can prevent colony death and natural selection can preserve strong Allee effects by selecting the traits with the largest investment on brood care and the lowest cannibalism rate. (6) Evolutionary dynamics may increase the fitness of the colony, i.e., the successful production of workforce which results in the increase of total worker population size, colony survival, and reproduction. Our results suggest both cannibalism and DOLs are adaptive strategies that increase the size of the worker population, and therefore, persistence of the colony.
Advanced literature analysis in a Big Data world
Authors: Cheadle Chris , Cao Hongbao , Kalinin Andrey , Hodgkinson Jaqui
Published: November 2016

Comprehensive data mining of the scientific literature has become an increasing challenge. To address this challenge, Elsevier's Pathway Studio software uses the techniques of natural language processing to systematically extract specific biological information from journal articles and abstracts that is then used to create a very large, structured, and constantly expanding literature knowledgebase. Highly sophisticated visualization tools allow the user to interactively explore the vast number of connections created and stored in the Pathway Studio database. We demonstrate the value of this structured information approach by way of a biomarker use case example and describe a comprehensive collection of biomarkers and biomarker candidates, as reported in the literature. We use four major neuropsychiatric diseases to demonstrate common and unique biomarker elements, demonstrate specific enrichment patterns, and highlight strategies for identifying the most recent and novel reports for potential biomarker discovery. Finally, we introduce an innovative new taxonomy based on brain region identifications, which greatly increases the potential depth and complexity of information retrieval related to, and now accessible for, neuroscience research.
Realising dignity in care home practice: an action research project
Authors: Gallagher Ann , Curtis Katherine , Dunn Michael , Baillie Lesley
Published: November 2016

Background

More than 400,000 older people reside in over 18,000 care homes in England. A recent social care survey found up to 50% of older people in care homes felt their dignity was undermined. Upholding the dignity of older people in care homes has implications for residents’ experiences and the role of Registered Nurses.

Aims and objectives

The study aimed to explore how best to translate the concept of dignity into care home practice, and how to support this translation process by enabling Registered Nurses to provide ethical leadership within the care home setting.

Design

Action research with groups of staff (Registered Nurses and non‐registered caregivers) and groups of residents and relatives in four care homes in the south of England to contribute to the development of the dignity toolkit.

Methods

Action research groups were facilitated by 4 researchers (2 in each care home) to discuss dignity principles and experiences within care homes. These groups reviewed and developed a dignity toolkit over six cycles of activity (once a month for 6 months). The Registered Nurses were individually interviewed before and after the activity.

Results

Hard copy and online versions of a dignity toolkit, with tailored versions for participating care homes, were developed. Registered Nurses and caregivers identified positive impact of making time for discussion about dignity‐related issues. Registered Nurses identified ongoing opportunities for using their toolkit to support all staff.

Conclusions

Nurses and caregivers expressed feelings of empowerment by the process of action research. The collaborative development of a dignity toolkit within each care home has the potential to enable ethical leadership by Registered Nurses that would support and sustain dignity in care homes.

Implications for practice

Action research methods empower staff to maintain dignity for older people within the care home setting through the development of practically useful toolkits to support everyday care practice. Providing opportunities for caregivers to be involved in such initiatives may promote their dignity and sense of being valued. The potential of bottom‐up collaborative approaches to promote dignity in care therefore requires further research.
Omenn Syndrome Presenting with Striking Erythroderma and Extreme Lymphocytosis in a Newborn
Authors: Zafar Rabia , Ver Heul Aaron , Beigelman Avraham , Bednarski Jeffrey J. , Bayliss Susan J. , Dehner Louis P. , Rosman Ilana S. , Coughlin Carrie C.
Published: November 2016

Omenn syndrome is an autosomal recessive form of “leaky” severe combined immune deficiency resulting in distinct phenotypic features. The patient described herein had an atypical presentation of Omenn syndrome, with conspicuous erythroderma and extreme lymphocytosis at birth, in contrast to the typical evolution of rash seen during the first few weeks of life. In addition, the skin findings were secondary to infiltration of CD8+ (cytotoxic) T‐cells in contrast to the CD4+ (helper) T‐cells typically seen, which broadens the Omenn syndrome phenotype.
Improving the Photocatalytic Activity of Modified Anatase TiO2 with Different Concentrations of Aluminum under Visible Light: Mechanistic Survey
Authors: Afshar Shahrara , Pordel Shabnam , Tahmouresilerd Babak , Azad Alireza
Published: November 2016

Visible light‐driven Al‐doped TiO2 with different aluminum contents (2, 5 and 10 mol%) were synthesized via a facile sol–gel method. Fourier transform infrared (FTIR), UV‐visible diffuse reflectance, energy dispersive X‐ray (EDX) spectroscopy as well as X‐ray diffraction (XRD), X‐ray fluorescence (XRF) and scanning electron microscopy (SEM) methods were used for the characterization of the obtained nanoparticles. The photocatalytic performance of the samples was evaluated by the degradation of rhodamine B (RhB) under visible light irradiation. The yield of the degradation RhB was estimated to be 71%, 89%, 65% and 56%, for the bare TiO2, 2%, 5% and 10% Al‐doped TiO2, respectively. It was found that 2 mol% of Al‐doped TiO2 shows the best photocatalytic performance. In low concentration of dopant, separation of photogenerated electron–hole pairs promoted, and subsequently, the degradation efficiency increased. It was proposed that the degradation of RhB by 2 mol% Al‐doped TiO2 photocatalyst follows both N‐deethylation and chromophore cleavage mechanisms, while the N‐deethylation still predominated over cleavage of dye chromophore structure. The key role of hydroxyl radicals in RhB degradation was verified by the effects of scavengers. In addition, the photocatalyst can be reused for three runs without any significant loss of its catalytic activity.
A Novel Streptavidin–luciferase Fusion Protein: Preparation, Properties and Application in Hybridization Analysis of DNA
Authors: Smirnova Daria V. , Rubtsova Maya Y. , Grigorenko Vitaly G. , Ugarova Natalia N.
Published: November 2016

A streptavidin–luciferase fusion protein comprising the thermostable mutant form of firefly luciferaseLuciola mingrelicaand minimal core streptavidin was constructed. The streptavidin–luciferase fusion was mainly produced in a tetrameric form with high luciferase and biotin‐binding activities. It was shown that fusion has the sameKmvalues forATPand luciferin and the bioluminescence spectra as initial luciferase. The linear dependence of the bioluminescence signal on the content of the fusion was observed within the range of 10−18–10−13mol per well. Successful application of obtained fusion in a biospecific bioluminescence assay based on biotin–streptavidin interactions was demonstrated by the example of a specificDNAhybridization analysis. ADNAhybridization analysis forEscherichia colicells identification was developed using unique for these cells gadB fragment encoding glutamate decarboxylase. The amplified biotinylated GadB fragments were hybridized with the immobilized oligonucleotide probes; then, the biotin in theDNAduplexes was detected using the streptavidin–luciferase fusion protein. To reach the high sensitivity of the assay, we optimized the conditions of the assay. It was shown that the use of Pluronic for plate modification resulted in a significant reduction in theDNAdetection limit which finally was 0.4 ng per well.
Bringing It All Together: Coupling Excision Repair to the DNA Damage Checkpoint
Authors: Lindsey‐Boltz Laura A.
Published: November 2016

Nucleotide excision repair and the ATR‐mediated DNA damage checkpoint are two critical cellular responses to the genotoxic stress induced by ultraviolet (UV) light and are important for cancer prevention. In vivo genetic data indicate that these global responses are coupled. Aziz Sancar et al. developed an in vitro coupled repair‐checkpoint system to analyze the basic steps of these DNA damage stress responses in a biochemically defined system. The minimum set of factors essential for repair‐checkpoint coupling include damaged DNA, the excision repair factors (XPA, XPC, XPF‐ERCC1, XPG, TFIIH, RPA), the 5′‐3′ exonuclease EXO1, and the damage checkpoint proteins ATR‐ATRIP and TopBP1. This coupled repair‐checkpoint system was used to demonstrate that the ~30 nucleotide single‐stranded DNA (ssDNA) gap generated by nucleotide excision repair is enlarged by EXO1 and bound by RPA to generate the signal that activates ATR.
Dissociating retrieval interference and reanalysis in the P600 during sentence comprehension
Authors: Tanner Darren , Grey Sarah , van Hell Janet G.
Published: November 2016

We investigated the relative independence of two key processes in language comprehension, as reflected in the P600 ERP component. Numerous studies have linked the P600 to sentence‐ or message‐level reanalysis; however, much research has shown that skilled, cue‐based memory retrieval operations are also important to successful language processing. Our goal was to identify whether these cue‐based retrieval operations are part of the reanalysis processes indexed by the P600. To this end, participants read sentences that were either grammatical or ungrammatical via subject‐verb agreement violations, and in which there was either no possibility for retrieval interference or there was an attractor noun interfering with the computation of subject‐verb agreement (e.g., “The slogan on the political poster(s) was/were …”). A stimulus onset asynchrony manipulation (fast, medium, or slow presentation rate) was designed to modulate participants' ability to engage in reanalysis processes. Results showed a reliable attraction interference effect, indexed by reduced behavioral sensitivity to ungrammaticalities and P600 amplitudes when there was an opportunity for retrieval interference, as well as an effect of presentation rate, with reduced behavioral sensitivity and smaller P600 effects at faster presentation rates. Importantly, there was no interaction between the two, suggesting that retrieval interference and sentence‐level reanalysis processes indexed by the P600 can be neurocognitively distinct processes.
The effect of the dynamics of knowledge base complexity on Schumpeterian patterns of innovation: the upstream petroleum industry
Authors: Maleki Ali , Rosiello Alessandro , Wield David
Published: November 2016

This article analyzes important changes in technological innovation in the upstream petroleum industry. It provides evidence that shifts in sectoral patterns of innovation over the petroleum industry's lifecycle from the 1970s up to 2005 were dependent on the dynamics of knowledge base complexity (KBC), a key dimension of an industry's technological regime. Accordingly, observed shifts in innovation patterns are understood to be the aggregated strategic response of industry innovators to changes in the technological regime. The article proposes a quantitative method for exploring KBC and Schumpeterian patterns of innovation, and interactions between the two at the industry level. As the industry evolved, its knowledge base moved to higher orders of complexity creating a shift in the Schumpeterian pattern of innovation. Increased KBC was found to alter Schumpeterian patterns from Mark I toward a ‘modified’ Mark II. Instead of coming predominantly from ‘traditional’ established oil operators, technological innovation was increasingly triggered by a new class of emergent integrated service companies – ‘second tier’ systems integrators of the upstream sector able to cope with increased KBC.
Decidualization of the canine uterus: From early until late gestational in vivo morphological observations, and functional characterization of immortalized canine uterine stromal cell lines
Authors: Graubner FR , Reichler IM , Rahman NA , Payan‐Carreira R , Boos A , Kowalewski MP
Published: November 2016

Contents

The apparent lack of classical mechanisms for maternal recognition of pregnancy is one of the most intriguing features of canine reproduction. Consequently, similar levels of circulating luteal steroids are observed in pregnant and non‐pregnant dogs. However, the early pre‐implantation canine embryo locally modulates uterine responses to its presence, facilitating the successful onset of pregnancy. As a part of this interaction, the canine uterus undergoes a species‐specific decidualization. Maternal stroma‐derived decidual cells develop, the only cells of the canine placenta expressing progesterone receptor (PGR). There exists an acute need for an in vitro stable cell line model for canine decidualization. Therefore, herein our goal was to establish, immortalize and characterize such a cell line. We immortalized three monolayer dog uterine stromal (DUS) cell lines by stably transfecting them with SV40Tag oncogene. Cells retained their mesenchymal character for over 30 passages, as evidenced by VIMENTIN staining. Genomic incorporation of the SV40Tag protein was confirmed by immunofluorescence and Western blot analyses. Cells submitted to a classical in vitro decidualization protocol (N6,2′‐O‐dibutyryladenosine‐3′,5′‐cyclic monophosphate) revealed upregulated gene levels of selected major decidualization markers (e.g. PRLR, PGR, IGF1, PTGES). Additionally, the basic decidualization capability of PGE2 was demonstrated, revealing increased levels of, for example, PGR and PRLR gene expression, thereby implying its involvement in the progesterone‐dependent decidualization in the canine uterus. In summary, our in vitro model with immortalized DUS cell line could serve as an ideal and unique model to study the underlying molecular and endocrine mechanisms of canine decidualization.
The nuclear and developmental competence of cumulus–oocyte complexes is enhanced by three‐dimensional coculture with conspecific denuded oocytes during in vitro maturation in the domestic cat model
Authors: Morselli MG , Luvoni GC , Comizzoli P
Published: November 2016

Contents

The objective of the study was to assess the efficacy of coculture with conspecific cumulus‐denuded oocytes (CDOs) during in vitro maturation in a three‐dimensional system of barium alginate microcapsules on the in vitro embryo development of domestic cat cumulus–oocyte complexes (COCs). In Experiment I, COCs were cocultured with conspecific CDOs or cultured separately in a 3D system for 24 hr of in vitro maturation, before assessing the meiotic progression. In Experiment II, the in vitro fertilization of COCs and CDOs was carried out with chilled epididymal spermatozoa and the presumptive zygotes were cultured in vitro separately for 7 days in 3D microcapsules before assesment of embryonic development. The results showed that the viability was maintained and that meiosis was resumed in the 3D culture system. The presence of CDOs during in vitro maturation improved the meiotic competence of the COCs, since the proportions of telophase I/metaphase II were higher than that in the groups cultured separately. The enrichment of the maturation system by companion oocytes also enhanced the ability of COCs to develop into embryos, and increased the percentages of morula and blastoycst stages. The COCs cocultured with CDOs developed at higher rates than the COCs cultured separately and the CDOs themselves. The beneficial effects of coculture with conspecific CDOs were presumably due to the paracrine action of some secreted factors that enhanced many molecular patterns related to the complex of cumulus oophorous cells. Further investigations to understand how the 3D microenvironment can influence the features of oocytes and embryos are required.
Fertility of Angus cross beef heifers after GnRH treatment on day 23 and timing of insemination in 14‐day CIDR protocol
Authors: Kasimanickam RK , Hall JB , Whittier WD
Published: November 2016

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This study compared artificial insemination pregnancy rate (AI‐PR) between 14‐day CIDR‐GnRH‐PGF2α‐GnRH and CIDR‐PGF2α‐GnRH synchronization protocol with two fixed AI times (56 or 72 hr after PGF2α). On day 0, heifers (n = 1311) from nine locations assigned body condition score (BCS: 1, emaciated; 9, obese), reproductive tract score (RTS: 1, immature, acyclic; 5, mature, cyclic) and temperament score (0, calm; and 1, excited) and fitted with a controlled internal drug release (CIDR, 1.38 g of progesterone) insert for 14 days. Within herd, heifers were randomly assigned either to no‐GnRH group (n = 635) or to GnRH group (n = 676), and heifers in GnRH group received 100 μg of GnRH (gonadorelin hydrochloride, IM) on day 23. All heifers received 25 mg of PGF2α (dinoprost, IM) on day 30 and oestrous detection aids at the same time. Heifers were observed for oestrus thrice daily until AI. Within GnRH groups, heifers were randomly assigned to either AI‐56 or AI‐72 groups. Heifers in AI‐56 group (n = 667) were inseminated at 56 hr (day 32 PM), and heifers in AI‐72 group (n = 644) were inseminated at 72 hr (day 33 AM) after PGF2α administration. All heifers were given 100 μg of GnRH concurrently at the time AI. Controlling for BCS (p < .05), RTS (p < .05), oestrous expression (p < .001), temperament (p < .001) and GnRH treatment by time of insemination (p < .001), the AI‐PR differed between GnRH treatment [GnRH (Yes – 60.9% (412/676) vs. No – 55.1% (350/635); p < .05)] and insemination time [AI‐56 – 54.6% (364/667) vs. AI‐72 – 61.8% (398/644); (p < .01)] groups. The GnRH treatment by AI time interaction influenced AI‐PR (GnRH56 – 61.0% (208/341); GnRH72 – 60.9% (204/335); No‐GnRH56 – 47.9% (156/326); No‐GnRH72 – 62.8% (194/309); p < .001). In conclusion, 14‐day CIDR synchronization protocol for FTAI required inclusion of GnRH on day 23 if inseminations were to be performed at 56 hr after PGF2α in order to achieve greater AI‐PR.
Estimation of endogenous levels of osteopontin, total antioxidant capacity and malondialdehyde in seminal plasma: Application for fertility assessment in buffalo (Bubalus bubalis) bulls
Authors: Kumar P , Saini M , Kumar D , Bharadwaj A , Yadav PS
Published: November 2016

Content

This study was attempted to identify subfertile bulls by quantifying the endogenous levels of osteopontin (OPN), total antioxidant capacity (TAC) and malondialdehyde (MDA) in seminal plasma of buffalo bulls. On the basis of conception rate, buffalo bulls were classified into two groups: high‐fertile (conception rate >50%) and subfertile bulls (conception rate <40%). A total of 100 ejaculates (10 ejaculates from each bull) were collected through artificial vagina method. The concentration ofOPN,TACand catalase (CAT) of high‐fertile bulls was found to be higher (p < .05) than that of subfertile bulls. Further,MDAlevel in seminal plasma was found to be lower (p < .05) in high‐fertile bulls compared with subfertile bulls. The fertility status had no effect on the superoxide dismutase (SOD) concentration in seminal plasma of both the groups. The levels ofOPN(r = .678,p = 0.013) andTAC(r = .648,p = .042) were found to be positively correlated with bull fertility and the level ofMDA(r = −.718,p = .019) was found to be negatively correlated with bull fertility. However, the fertility of bulls was not found to be significantly correlated withSOD,CATand sperm motility. In conclusion, seminalOPN,TACandMDAtended to be more realistic in identification of subfertile bulls from breeding herds.
A Multidimensional Poverty Index for Latin America
Authors: Santos Maria Emma , Villatoro Pablo
Published: November 2016

This paper proposes a new Multidimensional Poverty Index for Latin America. The index combines monetary and non‐monetary indicators, updates deprivation cut‐offs for certain traditional unsatisfied basic needs indicators and includes some new indicators, aiming to maximize regional comparability within the data constraints. The index is estimated for 17 countries of the region at two points in time—one around 2005 and the other around 2012. Overall, we estimate about 28 percent of people are multidimensionally poor in 2012 in the region. We find statistically significant reductions of poverty in most countries, both in terms of incidence and intensity over the period under analysis. However, important disparities between rural and urban areas remain. Statistical scrutiny of the index suggests that it captures the state of poverty relatively well while maintaining a certain parsimony and being highly robust to changes in weights, indicators, and poverty cut‐off.
Hidden Markov Modelling of Sparse Time Series from Non-Volcanic Tremor Observations
Authors: Wang Ting , Zhuang Jiancang , Obara Kazushige , Tsuruoka Hiroshi
Published: November 2016

Tremor activity has been recently detected in various tectonic areas world wide and is spatially segmented and temporally recurrent. We design a type of hidden Markov models to investigate this phenomenon, where each state represents a distinct segment of tremor sources. A mixture distribution of a Bernoulli variable and a continuous variable is introduced into the hidden Markov model to solve the problem that tremor clusters are very sparse in time. We applied our model to the tremor data from the Tokai region in Japan to identify distinct segments of tremor source regions and the results reveal the spatiotemporal migration pattern among these segments.
Forced Migration and Changing Livelihoods in the Brazilian Amazon
Authors: Randell Heather
Published: November 2016

Forced migration due to development projects or environmental change impacts livelihoods, as affected households are faced with new—and often less favorable—environmental, social, and economic conditions. This article examines changing livelihood strategies among a population of rural agricultural households displaced by the Belo Monte Dam in the Brazilian Amazon. Using longitudinal data, I find that many households used compensation payments to concentrate income generation efforts on the most lucrative strategies—cacao and cattle production and business or rental income. Poorer households and those that received the least compensation were more likely to continue relying on agricultural wage labor—a less desirable income source associated with not owning land or with persons needing to supplement income with additional work as a day laborer. Results also indicate that the amount of compensation received by most households was sufficient to enable them to make productive investments beyond attaining replacement land and housing. Many households invested in assets such as agricultural infrastructure, cattle, rental houses, or tractors—all of which directly contribute to future income. Displacement compensation, similar to remittances or conditional cash transfers, can therefore act as an important infusion of capital to promote socioeconomic development and poverty reduction.