bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake
Authors: Di Cesare Andrea , Eckert Ester M. , Teruggi Alessia , Fontaneto Diego , Bertoni Roberto , Callieri Cristiana , Corno Gianluca 
Published: June 2015

AbstractThe fate of antibiotic resistance genes (ARGs) in environmental microbial communities is of primary concern as prodromal of a potential transfer to pathogenic bacteria. Although of diverse origin, the persistence of ARGs in aquatic environments is highly influenced by anthropic activities, allowing potential control actions in well‐studied environments. However, knowledge of abundance and space–time distribution of ARGs in ecosystems is still scarce. Using quantitative real‐time PCR, we investigated the presence and the abundance of twelve ARGs (against tetracyclines, β‐lactams, aminoglycosides, quinolones and sulphonamides) at different sampling sites, depths and seasons, in Lake Maggiore, a large subalpine lake, and in the area of its watershed. We then evaluated the correlation between each ARG and a number of ecological parameters in the water column in the deepest part of the lake. Our results suggest the constitutive presence of at least four ARGs within the bacterial community with a high proportion of bacteria potentially resistant to tetracyclines and sulphonamides. The presence of these ARGs was independent of the total bacterial density and temperature. The dynamics of tet(A) and sulII genes were, however, positively correlated with dissolved oxygen and negatively to chlorophyll a, suggesting that the resistant microbes inhabit specific niches. These observations indicate that the lake is a reservoir of antibiotic resistances, highlighting the need of a deeper understanding of the sources of ARGs and the factors allowing their persistence in waters.
Transcriptome sequencing reveals both neutral and adaptive genome dynamics in a marine invader
Authors: Tepolt C. K. , Palumbi S. R. 
Published: June 2015

AbstractSpecies invasions cause significant ecological and economic damage, and genetic information is important to understanding and managing invasive species. In the ocean, many invasive species have high dispersal and gene flow, lowering the discriminatory power of traditional genetic approaches. High‐throughput sequencing holds tremendous promise for increasing resolution and illuminating the relative contributions of selection and drift in marine invasion, but has not yet been used to compare the diversity and dynamics of a high‐dispersal invader in its native and invaded ranges. We test a transcriptome‐based approach in the European green crab (Carcinus maenas), a widespread invasive species with high gene flow and a well‐known invasion history, in two native and five invasive populations. A panel of 10 809 transcriptome‐derived nuclear SNPs identified significant population structure among highly bottlenecked invasive populations that were previously undifferentiated with traditional markers. Comparing the full data set and a subset of 9246 putatively neutral SNPs strongly suggested that non‐neutral processes are the primary driver of population structure within the species’ native range, while neutral processes appear to dominate in the invaded range. Non‐neutral native range structure coincides with significant differences in intraspecific thermal tolerance, suggesting temperature as a potential selective agent. These results underline the importance of adaptation in shaping intraspecific differences even in high geneflow marine invasive species. They also demonstrate that high‐throughput approaches have broad utility in determining neutral structure in recent invasions of such species. Together, neutral and non‐neutral data derived from high‐throughput approaches may increase the understanding of invasion dynamics in high‐dispersal species.
Shoot bending promotes flower bud formation by miRNA‐mediated regulation in apple (Malus domestica Borkh.)
Authors: Xing Libo , Zhang Dong , Zhao Caiping , Li Youmei , Ma Juanjuan , An Na , Han Mingyu 
Published: July 2015

SummaryFlower induction in apple (Malus domestica Borkh.) trees plays an important life cycle role, but young trees produce fewer and inferior quality flower buds. Therefore, shoot bending has become an important cultural practice, significantly promoting the capacity to develop more flower buds during the growing seasons. Additionally, microRNAs (miRNAs) play essential roles in plant growth, flower induction and stress responses. In this study, we identified miRNAs potentially involved in the regulation of bud growth, and flower induction and development, as well as in the response to shoot bending. Of the 195 miRNAs identified, 137 were novel miRNAs. The miRNA expression profiles revealed that the expression levels of 68 and 27 known miRNAs were down‐regulated and up‐regulated, respectively, in response to shoot bending, and that the 31 differentially expressed novel miRNAs between them formed five major clusters. Additionally, a complex regulatory network associated with auxin, cytokinin, abscisic acid (ABA) and gibberellic acid (GA) plays important roles in cell division, bud growth and flower induction, in which related miRNAs and targets mediated regulation. Among them, miR396, 160, 393, and their targets associated with AUX, miR159, 319, 164, and their targets associated with ABA and GA, and flowering‐related miRNAs and genes, regulate bud growth and flower bud formation in response to shoot bending. Meanwhile, the flowering genes had significantly higher expression levels during shoot bending, suggesting that they are involved in this regulatory process. This study provides a framework for the future analysis of miRNAs associated with multiple hormones and their roles in the regulation of bud growth, and flower induction and formation in response to shoot bending in apple trees.
A Family of Potent Ru(II) Photosensitizers with Enhanced DNA Intercalation: Bimodal Photokillers
Authors: Pefkianakis Eleftherios K. , Theodossiou Theodossis A. , Toubanaki Dimitra K. , Karagouni Evdokia , Falaras Polycarpos , Papadopoulos Kyriakos , Vougioukalakis Georgios C. 
Published: June 2015

AbstractA new family of Ru(II)‐based photosensitizers was synthesized and systematically characterized. The ligands employed to coordinate the ruthenium metal center were the commercially available 2,2′‐bipyridine and a pyridine‐quinoline hybrid bearing an anthracene moiety. The complexes obtained carry either or Cl− counterions. These counterions determine the complexes' hydrophobic or hydrophilic character, respectively, therefore dictating their solubility in biologically related media. All photosensitizers exhibit characteristic, relatively strong and wide UV–Vis absorption spectral profiles. Their high efficiency in generating cytotoxic singlet oxygen was established (up to ΦΔ ~0.8). Moreover, the interaction of these photosensitizers with double‐stranded DNA was studied fluoro‐ and photospectroscopically and their binding affinities were found to be of the order of 3 × 107 M−1. All complexes are photocytotoxic to DU145 human prostate cancer cells. The highest light‐induced toxicity was conferred by the photosensitizers bearing Cl− counterions, probably due to the looser ionic “chaperoning” of Cl−, in comparison to , leading to higher cell internalization.
Effect of 808 nm Diode Laser on Swimming Behavior, Food Vacuole Formation and Endogenous ATP Production of Paramecium primaurelia (Protozoa)
Authors: Amaroli Andrea , Ravera Silvia , Parker Steven , Panfoli Isabella , Benedicenti Alberico , Benedicenti Stefano 
Published: June 2015

AbstractPhotobiomodulation (PBM) has been used in clinical practice for more than 40 years. To clarify the mechanisms of action of PBM at cellular and organism levels, we investigated its effect on Paramecium primaurelia (Protozoa) irradiated by an 808 nm infrared diode laser with a flat‐top handpiece (1 W in CW). Our results led to the conclusion that: (1) the 808 nm laser stimulates the P. primaurelia without a thermal effect, (2) the laser effect is demonstrated by an increase in swimming speed and in food vacuole formation, (3) the laser treatment affects endogenous adenosine triphosphate (ATP) production in a positive way, (4) the effects of irradiation dose suggest an optimum exposure time of 50 s (64 J cm−2 of fluence) to stimulate the Paramecium cells; irradiation of 25 s shows no effect or only mild effects and irradiation up to 100 s does not increase the effect observed with 50 s of treatment, (5) the increment of endogenous ATP concentration highlights the positive photobiomodulating effect of the 808 nm laser and the optimal irradiation conditions by the flat‐top handpiece.
Therapeutic Ultrasound as a Potential Male Dog Contraceptive: Determination of the Most Effective Application Protocol
Authors: Leoci R , Aiudi G , Silvestre F , Lissner EA , Marino F , Lacalandra GM 
Published: July 2015

ContentsUltrasound is one of the most promising forms of non‐invasive contraception and has been studied in several animal models. The objective of the current investigation was to determine the most practical and effective application protocol for dog sterilization. A total of 100 dogs were divided into five equal groups. Group A received 5‐min applications three times performed at 48‐hr intervals and covering the entire testicular area at frequency of 1 MHz; Group B received 5‐min applications three times performed at 48‐hr intervals over the dorso‐cranial area of the testis at frequency of 3 MHz; Group C received three sequential 5‐min applications (at 5‐min intervals between applications) covering the entire testicular area at frequency of 1 MHz; Group D received 15‐min applications two times performed at 48‐hr intervals and covering the entire testicular area at frequency of 1 MHz. The experimental groups' ultrasound had an intensity of 1.5W/cm2. The Control Group had the same procedure as Group A, but with the transducer switched‐off. Dogs were surgically castrated 40 days following the treatment for histological examination. Azoospermia, testicular volume reduction and apparently irreversible testicular damage were achieved by Group A. No effects were noticed in the other groups. Testosterone levels remained within physiological range with all application protocols. A regimen of three applications of ultrasound at 1 MHz, and 1.5 W/cm2, lasting 5 min with an interval of 48 h was effective as permanent sterilization in the dog without hormonal impact.
New Insights and Biomarkers for Type 1 Diabetes: Review for Scandinavian Journal of Immunology
Authors: Heinonen M. T. , Moulder R. , Lahesmaa R. 
Published: June 2015

AbstractThe increasing incidence of type 1 diabetes observed in the past 60 years has spawned massive efforts in multiple research fields to elucidate the aetiology of this disease. While GWAS studies provide a good genetic basis for the current knowledge, it is clear that environmental triggers and their influence in disease prevalence and origin are highly important. The realization of disease heterogeneity has created a requirement for better biomarkers to complement the known autoantibody markers and to more successfully predict the severity and onset time of the disease. Such biomarkers would be needed both for prevention as well as for monitoring disease activity and response to preventive and therapeutic measures. Systematic holistic approaches concentrating on the triggering molecular mechanisms, pancreatic beta cells, immune response, as well as the influence of diet and environment, are necessary to understand the disease pathogenesis and find a cure. The current genomic knowledge is being broadened with accompanying studies in epigenetics and transcriptomic regulation, metabolomics, proteomics and lipidomics, covering the whole system from beta cells, the profile and cellular balance of the infiltrating lymphocytes, to gut microbiota and viral infections. Here we highlight interesting recent findings in type 1 diabetes research.
CD21−/low B cells: A Snapshot of a Unique B Cell Subset in Health and Disease
Authors: Thorarinsdottir K. , Camponeschi A. , Gjertsson I. , Mårtensson I.‐L. 
Published: June 2015

AbstractB cells represent one of the cellular components of the immune system that protects the individual from invading pathogens. In response to the invader, these cells differentiate into plasma cells and produce large amounts of antibodies that bind to and eliminate the pathogen. A hallmark of autoimmune diseases is the production of autoantibodies i.e. antibodies that recognize self. Those that are considered pathogenic can damage tissues and organs, either by direct binding or when deposited as immune complexes. For decades, B cells have been considered to play a major role in autoimmune diseases by antibody production. However, as pathogenic autoantibodies appear to derive mainly from T cell dependent responses, T cells have been the focus for many years. The successful treatment of patients with autoimmune diseases with either B cell depletion therapy (rituximab) or inhibition of B cell survival (belimumab), suggested that not only the autoantibodies but also other B cell features are important. This has caused a surge of interest in B cells and their biology resulting in the identification of various subsets e.g. regulatory B cells, several memory B cell subsets etc. Also, in other conditions such as chronic viral infections and primary immunodeficiency, several B cell subsets with unique characteristics have been identified. In this review, we will discuss one of these subsets, a subset that is expanded in conditions characterized by chronic immune stimulation. This B cell subset lacks, or expresses low, surface levels of the complement receptor 2 (CD21) and has therefore been termed CD21−/low B cells.
Effect of long‐term prophylaxis in the development of cytomegalovirus‐specific T‐cell immunity in D+/R− solid organ transplant recipients
Authors: San‐Juan R. , Navarro D. , García‐Reyne A. , Montejo M. , Muñoz P. , Carratala J. , Len O. , Fortun J. , Muñoz‐Cobo B. , Gimenez E. , Eworo A. , Sabe N. , Meije Y. , Martín‐Davila P. , Andres A. , Delgado J. , Jimenez C. , Amat P. , Fernández‐Ruiz M. , López‐Medrano F. , Lumbreras C. , Aguado J.M. ,   REIPI Network
Published: July 2015

AbstractBackgroundThis study aimed to characterize the dynamics of acquisition of cytomegalovirus (CMV)‐specific cell‐mediated immunity (CMI) in CMV donor positive/recipient negative solid organ transplant (SOT) patients receiving long‐term antiviral prophylaxis, and to determine whether development of CMI confers protection against CMV disease.MethodsA prospective multicenter study was conducted in Spain from September 2009 to September 2012. Whole blood specimens were prospectively collected at 30, 90, 120, 200, and 365 days after SOT, and CMI was determined by enumeration of CMV pp65 and IE‐1‐specific CD69+/interferon‐γ‐producing CD8+ and CD4+ T cells by flow cytometry for intracellular cytokine staining. As part of a simultaneous clinical trial, patients received either early prophylaxis (in the first 3 days after transplantation) in the first period of the study or delayed prophylaxis (initiated at day 14) during the second period of the study. The impact of the dynamics of acquisition of CMV‐specific CMI on the incidence of CMV disease was evaluated by Kaplan–Meier survival analysis.ResultsA total of 95 SOT recipients were recruited. CMV infection and disease occurred in 38 (40%) and 26 (27.4%) patients, respectively. The proportion of patients achieving any detectable CMV‐specific CMI response at each of the different monitoring points was higher in liver transplant recipients, as compared to kidney or heart transplant recipients. The presence of any detectable response at day 120 or 200 was protective against the development of CMV disease (positive predictive values 92% and 93%, respectively).ConclusionsThe rate of acquisition of CMV‐specific CMI in SOT recipients undergoing antiviral prophylaxis differed significantly between different SOT populations. Patients developing any detectable CMI response were protected against the occurrence of CMV disease.
Allele frequencies of human platelet antigens in Banjar, Bugis, Champa, Jawa and Kelantan Malays in Peninsular Malaysia
Authors: Wan Syafawati W. U. , Norhalifah H. K. , Zefarina Z. , Zafarina Z. , Panneerchelvam S. , Norazmi M. N. , Chambers G. K. , Edinur H. A. 
Published: July 2015

SUMMARYObjectivesThe major aims of this study are to characterise and compile allelic data of human platelet antigen (HPA)‐1 to ‐6 and ‐15 systems in five Malay sub‐ethnic groups in Peninsular Malaysia.BackgroundHPAs are polymorphic glycoproteins expressed on the surface of platelet membranes and are genetically differentiated across ethnogeographically unrelated populations.MethodsBlood samples were obtained with informed consent from 192 volunteers: Banjar (n = 30), Bugis (n = 37), Champa (n = 51), Jawa (n = 39) and Kelantan (n = 35). Genotyping was done using polymerase chain reaction‐sequence specific primer method.ResultsIn general, frequencies of HPAs in the Malay sub‐ethnic groups are more similar to those in Asian populations compared with other more distinct populations such as Indians, Australian Aborigines and Europeans.ConclusionsThis study provides the first HPA datasets for the selected Malay sub‐ethnic groups. Subsequent analyses including previously reported HPA data of Malays, Chinese and Indians revealed details of the genetic relationships and ancestry of various sub‐populations in Peninsular Malaysia. Furthermore, the comprehensive HPA allele frequency information from Peninsular Malaysia provided in this report has potential applications for future study of diseases, estimating risks associated with HPA alloimmunization and for developing an efficient HPA‐typed donor recruitment strategy.
A conserved role for CUP‐SHAPED COTYLEDON genes during ovule development
Authors: Gonçalves Beatriz , Hasson Alice , Belcram Katia , Cortizo Millán , Morin Halima , Nikovics Krisztina , Vialette‐Guiraud Aurélie , Takeda Seiji , Aida Mitsuhiro , Laufs Patrick , Arnaud Nicolas 
Published: June 2015

SummaryThe evolution of plant reproductive strategies has led to a remarkable diversity of structures, especially within the flower, a structure characteristic of the angiosperms. In flowering plants, sexual reproduction depends notably on the development of the gynoecium that produces and protects the ovules. In Arabidopsis thaliana, ovule initiation is promoted by the concerted action of auxin with CUC1 (CUP‐SHAPED COTYLEDON1) and CUC2, two genes that encode transcription factors of the NAC family (NAM/ATAF1,2/CUC). Here we highlight an additional role for CUC2 and CUC3 in Arabidopsis thaliana ovule separation. While CUC1 and CUC2 are broadly expressed in the medial tissue of the gynoecium, CUC2 and CUC3 are expressed in the placental tissue between developing ovules. Consistent with the partial overlap between CUC1, CUC2 and CUC3 expression patterns, we show that CUC proteins can physically interact, both in yeast cells and in planta. We found that the cuc2;cuc3 double mutant specifically harbours defects in ovule separation, producing fused seeds that share the seed coat, and suggesting that CUC2 and CUC3 promote ovule separation in a partially redundant manner. Functional analyses show that CUC transcription factors are also involved in ovule development in Cardamine hirsuta. Additionally we show a conserved expression pattern of CUC orthologues between ovule primordia in other phylogenetically distant species with different gynoecium architectures. Taken together these results suggest an ancient role for CUC transcription factors in ovule separation, and shed light on the conservation of mechanisms involved in the development of innovative structures.
JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis
Authors: Deng Shulin , Xu Jun , Liu Jun , Kim Sang‐Hee , Shi Suhua , Chua Nam‐Hai 
Published: June 2015

SummaryTransposable elements (TEs) and repetitive sequences are ubiquitously present in eukaryotic genomes which are in general epigenetically silenced by DNA methylation and/or histone 3 lysine 9 methylation (H3K9me). RNA‐directed DNA methylation (RdDM) is the major pathway that initiates de novo DNA methylation in Arabidopsis and sets up a self‐reinforcing silencing loop between DNA methylation and H3K9me. However, a key issue is the requirement of a basal level transcript from the target loci to initiate the RNA‐based silencing. How the heterochromatic silenced loci are transcribed remains largely unknown. Here, we show that JMJ24, a JmjC domain‐containing protein counteracts H3K9me to promote basal level transcription of endogenous silenced loci in Arabidopsis. JMJ24 functionally resembles the fission yeast JmjC protein Epe1. The transcript promoted by JMJ24 is, at least in part, processed to small RNA to initiate the RdDM. Genome‐wide transcriptome profiling indicates that transcript levels of TEs are more likely regulated by JMJ24, compared with protein‐coding genes. Our data suggest that JMJ24 plays a conserved role in promoting basal level transcription of endogenous silenced loci to reinforce the silencing. We also provide evidence of a physical association between JMJ24 and RNA‐dependent RNA polymerase 2 (RDR2), which represents an evolved property of the RNA silencing pathway.
Exploring diterpene metabolism in non‐model species: transcriptome‐enabled discovery and functional characterization of labda‐7,13E‐dienyl diphosphate synthase from Grindelia robusta
Authors: Zerbe Philipp , Rodriguez Selina M. , Mafu Sibongile , Chiang Angela , Sandhu Harpreet K. , O'Neil‐Johnson Mark , Starks Courtney M. , Bohlmann Jörg 
Published: June 2015

SummaryGrindelia robusta or gumweed, is a medicinal herb of the sunflower family that forms a diverse suite of diterpenoid natural products. Its major constituents, grindelic acid and related grindelane diterpenoids accumulate in a resinous exudate covering the plants’ surfaces, most prominently the unopened composite flower. Recent studies demonstrated potential pharmaceutical applications for grindelic acid and its synthetic derivatives. Mining of the previously published transcriptome of G. robusta flower tissue identified two additional diterpene synthases (diTPSs). We report the in vitro and in vivo functional characterization of an ent‐kaurene synthase of general metabolism (GrTPS4) and a class II diTPS (GrTPS2) of specialized metabolism that converts geranylgeranyl diphosphate (GGPP) into labda‐7,13E‐dienyl diphosphate as verified by nuclear magnetic resonance (NMR) analysis. Tissue‐specific transcript abundance of GrTPS2 in leaves and flowers accompanied by the presence of an endocyclic 7,13 double bond in labda‐7,13E‐dienyl diphosphate suggest that GrTPS2 catalyzes the first committed reaction in the biosynthesis of grindelic acid and related grindelane metabolites. With the formation of labda‐7,13E‐dienyl diphosphate, GrTPS2 adds an additional function to the portfolio of monofunctional class II diTPSs, which catalytically most closely resembles the bifunctional labda‐7,13E‐dien‐15‐ol synthase of the lycopod Selaginella moellendorffii. Together with a recently identified functional diTPS pair of G. robusta producing manoyl oxide, GrTPS2 lays the biosynthetic foundation of the diverse array of labdane‐related diterpenoids in the genus Grindelia. Knowledge of these natural diterpenoid metabolic pathways paves the way for developing biotechnology approaches toward producing grindelic acid and related bioproducts.