bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe psoriasis entering remission after treatment for latent tuberculosis with isoniazid: Report of two cases
Authors: Partarrieu‐Mejías Felipe , Hernández‐Bel Pablo , Giácaman‐von der Weth Macarena , Pérez‐Ferriols Amparo 
Published: July 2019

AbstractPsoriasis is a multifactorial systemic disease with predominantly cutaneous manifestations. The role of tuberculosis infection in the pathogenesis of psoriasis has not been consistently proven. Current guidelines recommend screening for tuberculosis infection in any patient with psoriasis when the initiation of biologic therapy is being considered. Isoniazid is an antibiotic with high bactericidal effect on replicating mycobacteria and constitutes the most commonly prescribed treatment for latent tuberculosis infection. Here, we report two cases of patients with psoriasis who presented at our clinic with extensive cutaneous involvement despite previous treatments with topical and systemic therapies. Both were considered as candidates for biologic therapy. As part of the screening protocol, a tuberculin test was performed with a positive result. In the absence of symptoms and chest radiography findings, isoniazid 300 mg/day for 6 months was prescribed to treat latent tuberculosis infection. This resulted in significant clearing of their skin lesions in the absence of any other concurrent treatment, apart from emollients. Both patients remained clinically stable and with no need of further systemic treatment. This situation has only been described twice before in the English‐language published work. These cases highlight the possible role of tuberculosis infection in the pathogenesis of psoriasis, suggesting the possible existence of a link between untreated infection and skin lesions. This can lead to consideration of novel therapeutic strategies and new lines of investigation.
Interspecific plant competition mediates the metabolic and ecological signature of a plant–herbivore interaction under warming and elevated CO2
Authors: Van De Velde Helena , AbdElgawad Hamada , Asard Han , Beemster Gerrit T. S. , Selim Samy , Nijs Ivan , Bonte Dries 
Published: July 2019

Abstract

Biotic interactions shape community evolution, but we lack mechanistic insights on how metabolic and ecological processes under climate change are altered by biotic interactions.

We used a two‐trophic model community consisting of the aphid Dysaphis plantaginea feeding on the forb Plantago lanceolata, and a grass competitor Lolium perenne that does not experience herbivory by the aphid. Monocultures and mixtures were exposed to the herbivory treatment and to three relevant simulated environmental changes as prevalent under current climate change (increased temperature, CO2, and increased temperature and CO2)

Elevated CO2 reduced the nitrogen content of P. lanceolata, while simultaneous increases of CO2 and temperature modified the plant metabolic component and the magnitude of these responses in different directions. Elevated CO2 enhanced defence systems in P. lanceolata, but these effects were not altered by warming. Interspecific plant competition did, however, neutralize these responses. There were no indirect effects of climate change on aphid population growth despite changes in plant defence, nutritional quality and biomass induced by our environmental change scenarios.

We thus demonstrate interactions between abiotic and biotic processes on plant metabolite profiles, but more importantly, that climate change effects on a selection of the metabolic pathways are altered by herbivory and competition. Our experiment under semi‐natural conditions thus demonstrates the non‐additive and often neutralizing effects of biotic interactions on plant metabolism and species performance under climate‐associated environmental change.

A free Plain Language Summary can be found within the Supporting Information of this article.
The effects of increasing land use intensity on soil nematodes: A turn towards specialism
Authors: Vazquez Carmen , de Goede Ron G. M. , Korthals Gerard W. , Rutgers Michiel , Schouten Anton J. , Creamer Rachel 
Published: July 2019

Abstract

The ecosystem services that humans obtain from the soil are strongly linked to the soil's biota. There is ample evidence that intensive agriculture has a negative effect on the soil's biological diversity. While in other ecosystems, habitat specialists are at a higher risk of extinction due to human impacts than generalists, we have no evidence of whether this holds true for soil biota. We calculated the realized niche width for soil nematodes using co‐occurrence data. We compared these with ecological traits. We then calculated an index of community specialization and tested whether land use intensity leads to decreases in the index of community specialization, taxon richness, diversity and to changes in nematode abundance.

The resulting realized niche widths did not correlate with ecological traits such as feeding group, body mass or c‐p class. While it is possible that there are no relationships between these traits and the realized niche width, it is likelier that food availability, pH tolerance, or host breadth are more important factors in explaining niche width.

Contrary to our expectations, the lowest community specialization levels were found in soils with the lowest human intervention (shrubland–woodland ecosystems), while grasslands, dairy farms and arable farms had an overall higher level of specialization. Weather variables and land use intensity explained 66% of the variation in the index of community specialization in sandy soils. We found highest richness and diversity at intermediate levels of disturbance (grasslands and dairy farms). The lowest abundances were found on shrubland–woodland systems. Dairy farms on sand and clay had similar indices of community specialization, whereas peaty soils fostered a higher proportion of habitat specialists.

We argue that farmland supposes a stable environment for organisms with shorter life spans. Agricultural management strives to lower disturbances, allowing shorter lived organisms to escape pressures otherwise present in nature, such as drought or nutrient deficiencies during the growing season. In very disturbed systems, however, specialists may also suffer from negative effects of land use intensity.

This co‐occurrence method to assess niche width opens the door to estimating the soil community's niche breadth, for which resource‐based methods are difficult to implement.

A free Plain Language Summary can be found within the Supporting Information of this article.
Dietary restriction and insulin‐like signalling pathways as adaptive plasticity: A synthesis and re‐evaluation
Authors: Regan Jennifer C. , Froy Hannah , Walling Craig A. , Moatt Joshua P. , Nussey Daniel H. 
Published: July 2019

Abstract

Dietary restriction (DR) under laboratory conditions generally extends life span and delays ageing across species as diverse as yeast, nematode worms, flies and mice, and is underpinned by taxonomically conserved physiological pathways, notably the insulin‐like signalling pathway (IIS). Despite growing excitement about the links between DR/IIS and ageing within biogerontology, our understanding of why the DR response and associated pathways evolved under natural selection remains controversial and limited.

Here, we provide a brief overview of current understanding of the relationship between DR and IIS and ageing from modern biogerontology and go on to summarize the evidence that the IIS pathway integrates a range of important environmental cues including photoperiod, temperature and humidity, as well as nutrition.

We go on to discuss the main existing evolutionary explanations for DR and argue that they are not mutually exclusive and are too nutrition‐focussed to fully explain the evolutionary origin of the IIS pathway. In the wild, environmental cues and pressures are dynamic and multivariate, and physiological pathways capable of integrating multiple predictive cues could be strongly favoured by natural selection.

We hypothesize that the IIS and related pathways, such as mTOR, evolved to detect and integrate a wide range of environmental cues (not just diet) that are predictive of important selective pressures in the wild. Available evidence suggests the pathway is capable of triggering a range of phenotypic responses, depending on the cues provided, ranging from profound physiological remodelling (e.g. diapause, aestivation, hibernation) associated with promoting survival through challenging environments, to more subtle responses to acute, fine‐scale variation in the environment which may allow individuals to better match their level of reproductive investment to their conditions.

We argue that the IIS pathway underpins important adaptive phenotypic plastic responses to a wide range of environmental inputs, of which diet is just one. A multi‐disciplinary approach combining perspectives and methods from biogerontology, cell biology, ecology and evolutionary biology will be essential to develop our understanding of the evolutionary origins of this pathway and the way natural selection and the environment have shaped variation in the IIS pathway's response to different environmental cues.

A free Plain Language Summary can be found within the Supporting Information of this article.
Host genetics and geography influence microbiome composition in the spongeIrcinia campana
Authors: Griffiths Sarah M. , Antwis Rachael E. , Lenzi Luca , Lucaci Anita , Behringer Donald C. , Butler Mark J. , Preziosi Richard F. 
Published: July 2019

AbstractMarine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome.Here, we examined the influence of genetic variation and geographic location on the composition of theIrcinia campanamicrobiome.We developed new microsatellite markers to genotypeI. campanafrom two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing.We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that althoughI. campanawas not genetically differentiated between sites, microbiome composition differed by location.Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco‐evolutionary dynamics of host‐associated microbiomes.
Bacterial colonization of minerals in grassland soils is selective and highly dynamic
Authors: Vieira Selma , Sikorski Johannes , Gebala Aurelia , Boeddinghaus Runa S. , Marhan Sven , Rennert Thilo , Kandeler Ellen , Overmann Jörg 
Published: July 2019

SummaryBacteria colonize reactive minerals in soils where they contribute to mineral weathering and transformation. So far, the specificity, patterns and dynamics of mineral colonization have rarely been assessed under natural conditions. High throughput Illumina sequencing was employed to investigate the bacterial communities assembling on illite and goethite during exposure to natural grassland soils. Two different types of organic carbon sources, simple carbon compounds representing root exudates and detritus of two dominant grassland plant species were applied, and their effects on the temporal dynamics of bacterial communities were investigated. The observed temporal patterns suggest that the surfaces of de novo exposed minerals in soils drive the establishment of bacterial communities and override the effect of the type of carbon sources and of other environmental properties. Mineral colonization was selective and specific bacterial sequence variants exhibited distinct colonization patterns, among which early, intermittent, and late colonizers could be distinguished. Based on our results, soil minerals are not only colonized by specific bacterial communities but enable a succession of different bacterial communities. Our results thereby expand the concept of the mineralosphere and provide novel insights into mechanisms of community assembly in the soil ecosystem.
JR‐131, a Biosimilar of Darbepoetin Alfa, for the Treatment of Hemodialysis Patients With Renal Anemia: A Randomized, Double‐Blinded, Parallel‐Group Phase 3 Study
Authors: Nishi Shinichi , Yamada Masayuki , Tsuruya Kazuhiko , Masakane Ikuto , Nakamoto Hidetomo 
Published: July 2019

AbstractThe aim of this study was to compare the efficacy and safety of intravenous JR‐131, a darbepoetin alfa biosimilar, to darbepoetin alfa in hemodialysis patients with renal anemia. In this 24‐week, multicenter, randomized, double‐blinded, parallel‐group phase 3 study, 334 hemodialysis patients with renal anemia who had been receiving darbepoetin alfa were randomized to either JR‐131 or darbepoetin alfa group. The initial dose was set based on the darbepoetin alfa dose during the observation period. The primary endpoint was change in hemoglobin level from baseline to end of treatment. The 95% confidence interval of the difference in the change in hemoglobin level between the groups was −0.19 to −0.20 g/dL, within the equivalent margin of −0.5 to 0.5 g/dL. No notable treatment‐emergent adverse events were observed in either group. JR‐131 was therapeutically equivalent to darbepoetin alfa, and the safety profile of JR‐131 was similar to that of darbepoetin alfa.
Genome‐skimming provides accurate quantification for pollen mixtures
Authors: Lang Dandan , Tang Min , Hu Jiahui , Zhou Xin 
Published: July 2019

AbstractStudies on foraging partitioning in pollinators can provide critical information to the understanding of food‐web niche and pollination functions, thus aiding conservation. Metabarcoding based on PCR amplification and high‐throughput sequencing has seen increasing applications in characterizing pollen loads carried by pollinators. However, amplification bias across taxa could lead to unpredictable artefacts in estimation of pollen compositions. We examined the efficacy of a genome‐skimming method based on direct shotgun sequencing in quantifying mixed pollen, using mock samples (five and 14 mocks of flower and bee pollen, respectively). The results demonstrated a high level of repeatability and accuracy in identifying pollen from mixtures of varied species ratios. All pollen species were detected in all mocks, and pollen frequencies estimated from the number of sequence reads of each species were significantly correlated with pollen count proportions (linear model, R2 = 86.7%, p = 2.2e−16). For >97% of the mixed taxa, pollen proportion could be quantified by sequencing to the correct order of magnitude, even for species which constituted only 0.2% of the total pollen. In addition, DNA extracted from pollen grains equivalent to those collected from a single honeybee corbicula was sufficient for genome‐skimming. We conclude that genome‐skimming is a feasible approach to identifying and quantifying mixed pollen samples. By providing reliable and sensitive taxon identification and relative abundance, this method is expected to improve our understanding in studies that involve plant–pollinator interactions, such as pollen preference in corbiculate bees, pollen diet analyses and identification of landscape pollen resource use from beehives.
Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real‐time PCR analyses
Authors: Yourick Miranda R. , Sandkam Benjamin A. , Gammerdinger William J. , Escobar‐Camacho Daniel , Nandamuri Sri Pratima , Clark Frances E. , Joyce Brendan , Conte Matthew A. , Kocher Thomas D. , Carleton Karen L. 
Published: July 2019

AbstractTo determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.
Characterizing symbiont inheritance during host–microbiota evolution: Application to the great apes gut microbiota
Authors: Perez‐Lamarque Benoît , Morlon Hélène 
Published: July 2019

AbstractMicrobiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes’ diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model‐based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high‐throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.
Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions
Authors: Billerman Shawn M. , Walsh Jennifer 
Published: July 2019

AbstractMuseum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.
Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells
Authors: Zhou Jiajian , So Karl K. , Li Yuying , Li Yang , Yuan Jie , Ding Yingzhe , Chen Fengyuan , Huang Yile , Liu Jin , Lee Wayne , Li Gang , Ju Zhenyu , Sun Hao , Wang Huating 
Published: July 2019

AbstractEpigenetic alterations occur in various cells and tissues during aging, but it is not known if such alterations are also associated with aging in skeletal muscle. Here, we examined the changes of a panel of histone modifications and found H3K27ac (an active enhancer mark) is markedly increased in aged human skeletal muscle tissues. Further analyses uncovered that the H3K27ac increase and enhancer activation are associated with the up‐regulation of extracellular matrix (ECM) genes; this may result in alteration of the niche environment for skeletal muscle stem cells, also called satellite cells (SCs), which causes decreased myogenic potential and fibrogenic conversion of SCs. In mice, treatment of aging muscles with JQ1, an inhibitor of enhancer activation, inhibited the ECM up‐regulation and fibrogenic conversion of SCs and restored their myogenic differentiation potential. Altogether, our findings not only uncovered a novel aspect of skeletal muscle aging that is associated with enhancer remodeling but also implicated JQ1 as a potential treatment approach for restoring SC function in aging muscle.
Opacity and the comovement in the stock prices of banks
Authors: Blau Benjamin M. , Griffith Todd G. , Whitby Ryan J. 
Published: July 2019

AbstractWe examine whether the stock prices of banks co‐move more than the stock prices of non‐banks, and whether that comovement is driven by informational opacity. Since the risks associated with the financial intermediation process are relatively opaque to outside investors, valuing banks can be difficult and information acquisition can be costly. We introduce a measure of comovement, denoted as beta dispersion, that identifies how closely a particular stock co‐moves with the average industry CAPM beta. We find that bank stock prices generally co‐move more than non‐bank stock prices, and that opacity is driving the higher levels of comovement.