bluuebunny/crossref_metadata_2025_split huggingface dataset:
A large family of anti‐activators accompanying XylS/AraC family regulatory proteins
Authors: Santiago Araceli E. , Yan Michael B. , Tran Minh , Wright Nathan , Luzader Deborah H. , Kendall Melissa M. , Ruiz‐Perez Fernando , Nataro James P. 
Published: April 2016

SummaryAraC Negative Regulators (ANR) suppress virulence genes by directly down‐regulating AraC/XylS members in Gram‐negative bacteria. In this study, we sought to investigate the distribution and molecular mechanisms of regulatory function for ANRs among different bacterial pathogens. We identified more than 200 ANRs distributed in diverse clinically important gram negative pathogens, including Vibrio spp., Salmonella spp., Shigella spp., Yersinia spp., Citrobacter spp., enterotoxigenic (ETEC) and enteroaggregative E. coli (EAEC), and members of the Pasteurellaceae. By employing a bacterial two hybrid system, pull down assays and surface plasmon resonance (SPR) analysis, we demonstrate that Aar (AggR‐activated regulator), a prototype member of the ANR family in EAEC, binds with high affinity to the central linker domain of AraC‐like member AggR. ANR‐AggR binding disrupted AggR dimerization and prevented AggR‐DNA binding. ANR homologs of Vibrio cholerae, Citrobacter rodentium, Salmonella enterica and ETEC were capable of complementing Aar activity by repressing aggR expression in EAEC strain 042. ANR homologs of ETEC and Vibrio cholerae bound to AggR as well as to other members of the AraC family, including Rns and ToxT. The predicted proteins of all ANR members exhibit three highly conserved predicted α‐helices. Site‐directed mutagenesis studies suggest that at least predicted α‐helices 2 and 3 are required for Aar activity. In sum, our data strongly suggest that members of the novel ANR family act by directly binding to their cognate AraC partners.
An effector of apple proliferation phytoplasma targets TCP transcription factors—a generalized virulence strategy of phytoplasma?
Authors: Janik Katrin , Mithöfer Axel , Raffeiner Margot , Stellmach Hagen , Hause Bettina , Schlink Katja 
Published: April 2016

SummaryThe plant pathogen Candidatus Phytoplasma mali (P. mali) is the causative agent of apple proliferation, a disease of increasing importance in apple‐growing areas within Europe. Despite its economic importance, little is known about the molecular mechanisms of disease manifestation within apple trees. In this study, we identified two TCP (TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR) transcription factors of Malus x domestica as binding partners of the P. mali SAP11‐like effector ATP_00189. Phytohormone analyses revealed an effect of P. mali infection on jasmonates, salicylic acid and abscisic acid levels, showing that P. mali affects phytohormonal levels in apple trees, which is in line with the functions of the effector assumed from its binding to TCP transcription factors. To our knowledge, this is the first characterization of the molecular targets of a P. mali effector and thus provides the basis to better understand symptom development and disease progress during apple proliferation. As SAP11 homologues are found in several Phytoplasma species infecting a broad range of different plants, SAP11‐like proteins seem to be key players in phytoplasmal infection.
Sensory innervation of the guinea pig colon and rectum compared using retrograde tracing and immunohistochemistry
Authors: Chen B. N. , Olsson C. , Sharrad D. F. , Brookes S. J. H. 
Published: April 2016

AbstractBackgroundNeurons in lumbar and sacral dorsal root ganglia (DRG) comprise extrinsic sensory pathways to the distal colon and rectum, but their relative contributions are unclear. In this study, sensory innervation of the rectum and distal colon in the guinea pig was directly compared using retrograde labeling combined with immunohistochemistry.MethodsThe lipophilic tracer, DiI, was injected in either the rectum or distal colon of anesthetized guinea pigs, then DRG (T6 to S5) and nodose ganglia were harvested and labeled using antisera for calcitonin gene‐related peptide (CGRP) and transient receptor potential vanilloid 1(TRPV1).Key ResultsMore primary afferent cell bodies were labeled from the rectum than from the distal colon. Vagal sensory neurons, with cell bodies in the nodose ganglia comprised fewer than 0.5% of labeled sensory neurons. Spinal afferents to the distal colon were nearly all located in thoracolumbar DRG, in a skewed unimodal distribution (peak at L2); fewer than 1% were located in sacral ganglia. In contrast, spinal afferents retrogradely labeled from the rectum had a bimodal distribution, with one peak at L3 and another at S2. Fewer than half of all retrogradely labeled spinal afferent neurons were immunoreactive for CGRP or TRPV1 and these included the larger traced neurons, especially in thoracolumbar ganglia.Conclusions & InferencesIn the guinea pig, both the distal colon and the rectum receive a sensory innervation from thoracolumbar ganglia. Sacral afferents innervate the rectum but not the distal colon. Calcitonin gene‐related peptide immunoreactivity was detectable in fewer than half of afferent neurons in both pathways.
Practical and reproducible estimation of myenteric interstitial cells of Cajal in the bowel for diagnostic purposes
Authors: den Braber‐Ymker M. , Heijker S. , Lammens M. , Nagtegaal I. D. 
Published: April 2016

AbstractBackgroundHistological assessment of the interstitial cells of Cajal (ICCs) in the bowel is important for diagnosing patients with gastrointestinal neuromuscular diseases (GINMD). Although the International Working Group on GINMD proposed reporting a decrease in ICC number of more than 50%, quantitative methods used in literature are not practical for daily routine of the pathologist. Consequently, this study presents a straightforward semiquantitative estimation method for myenteric ICCs of the bowel.MethodsFormalin‐fixed paraffin‐embedded sections from small bowel (n = 87) and colon (n = 159) were collected to create two control groups and four groups composed of patients with gastrointestinal motility disorders. The control groups included material of resection and autopsy origin, respectively. Samples were stained with CD117 (c‐kit) antibody to estimate the myenteric ICC network. Scores of two observers were compared to analyze inter‐ and intraobserver agreement and reliability.Key ResultsInterobserver reliability was almost perfect for small bowel (intraclass correlation coefficient 0.847; 95% confidence interval [CI]: 0.774–0.897) and substantial for colon (0.683; 95% CI: 0.591–0.758). Almost perfect intraobserver reliability was found (intraclass correlation coefficient 0.918; 95% CI: 0.874–0.947). The small bowel showed more myenteric ICCs than the colon. Neither significant differences between colonic regions were found nor were there any differences in the orientation of the sections.Conclusions & InferencesThe proposed estimation method for the myenteric ICC network showed generally good agreement and reliability. As the method is semiquantitative, simple, and capable to differentiate between normal and diseased tissue, it can be used in routine diagnostics of gastrointestinal neuromuscular disorders.
Using codispersion analysis to quantify and understand spatial patterns in species–environment relationships
Authors: Buckley Hannah L. , Case Bradley S. , Zimmerman Jess K. , Thompson Jill , Myers Jonathan A. , Ellison Aaron M. 
Published: April 2016

Summary

The analysis of spatial patterns in species–environment relationships can provide new insights into the niche requirements and potential co‐occurrence of species, but species abundance and environmental data are routinely collected at different spatial scales. Here, we investigate the use of codispersion analysis to measure and assess the scale, directionality and significance of complex relationships between plants and their environment in large forest plots.

We applied codispersion analysis to both simulated and field data on spatially located tree species basal area and environmental variables. The significance of the observed bivariate spatial associations between the basal area of key species and underlying environmental variables was tested using three null models.

Codispersion analysis reliably detected directionality (anisotropy) in bivariate species–environment relationships and identified relevant scales of effects. Null model‐based significance tests applied to codispersion analyses of forest plot data enabled us to infer the extent to which environmental conditions, tree sizes and/or tree spatial positions underpinned the observed basal area–environment relationships, or whether relationships were a result of other unmeasured factors.

Codispersion analysis, combined with appropriate null models, can be used to infer hypothesized ecological processes from spatial patterns, allowing us to start disentangling the possible drivers of plant species–environment relationships.
Double‐stranded RNAs induce a pattern‐triggered immune signaling pathway in plants
Authors: Niehl Annette , Wyrsch Ines , Boller Thomas , Heinlein Manfred 
Published: April 2016

Summary

Pattern‐triggered immunity (PTI) is a plant defense response that relies on the perception of conserved microbe‐ or pathogen‐associated molecular patterns (MAMPs or PAMPs, respectively). Recently, it has been recognized that PTI restricts virus infection in plants; however, the nature of the viral or infection‐induced PTI elicitors and the underlying signaling pathways are still unknown.

As double‐stranded RNAs (dsRNAs) are conserved molecular patterns associated with virus replication, we applied dsRNAs or synthetic dsRNA analogs to Arabidopsis thaliana and investigated PTI responses.

We show that in vitro‐generated dsRNAs, dsRNAs purified from virus‐infected plants and the dsRNA analog polyinosinic–polycytidylic acid (poly(I:C)) induce typical PTI responses dependent on the co‐receptor SOMATIC EMBRYOGENESIS RECEPTOR‐LIKE KINASE 1 (SERK1), but independent of dicer‐like (DCL) proteins in Arabidopsis. Moreover, dsRNA treatment of Arabidopsis induces SERK1‐dependent antiviral resistance. Screening of Arabidopsis wild accessions demonstrates natural variability in dsRNA sensitivity.

Our findings suggest that dsRNAs represent genuine PAMPs in plants, which induce a signaling cascade involving SERK1 and a specific dsRNA receptor. The dependence of dsRNA‐mediated PTI on SERK1, but not on DCLs, implies that dsRNA‐mediated PTI involves membrane‐associated processes and operates independently of RNA silencing. dsRNA sensitivity may represent a useful trait to increase antiviral resistance in cultivated plants.
Early tooth loss in end‐stage renal disease patients on haemodialysis
Authors: Limeres J , Garcez JF , Marinho JS , Loureiro A , Diniz M , Diz P 
Published: April 2016

ObjectiveThis article sets out to evaluate the prevalence and aetiopathogenesis of edentulism in patients on haemodialysis.Subjects and methodsThe study group comprised 44 adult patients with end‐stage renal disease (ESRD) on haemodialysis. A control group was formed of 44 individuals matched for age and sex and with a glomerular filtration rate >90 ml min−1. All participants underwent intra‐oral examination, gathering information on dental and periodontal status, and a saliva sample was taken to determine saliva debit and its biochemical composition.ResultsThe average number of missing teeth was higher in ESRD patients than in controls (P = 0.018). Six (13.6%) fully edentulous individuals were detected in the study group and 1 (2.2%) in the control group. Some of the clinical and biochemical variables with statistically significant differences between the study group and the control group showed a significant relationship with the number of missing teeth, but the depth of the periodontal pockets presented the highest coefficient of determination (OR = 3511.1; 95%CI = 82.2–6834.3; P < 0.001; R2 = 0.827).ConclusionsPremature tooth loss is common in haemodialysis patients. Although the aetiology and pathogenesis of this finding has still not been fully clarified, it appears that severe periodontal disease may play a relevant role.
Inactivation of the spxA1 or spxA2 gene of Streptococcus mutans decreases virulence in the rat caries model
Authors: Galvão L.C.C. , Rosalen P.L. , Rivera‐Ramos I. , Franco G.C.N. , Kajfasz J.K. , Abranches J. , Bueno‐Silva B. , Koo H. , Lemos J.A. 
Published: April 2016

SummaryIn oral biofilms, the major environmental challenges encountered by Streptococcus mutans are acid and oxidative stresses. Previously, we showed that the transcriptional regulators SpxA1 and SpxA2 are involved in general stress survival of S. mutans with SpxA1 playing a primary role in activation of antioxidant and detoxification strategies whereas SpxA2 serves as a back up activator of oxidative stress genes. We have also found that spxA1 mutant strains (∆spxA1 and ∆spxA1∆spxA2) are outcompeted by peroxigenic oral streptococci in vitro and have impaired abilities to colonize the teeth of rats fed a highly cariogenic diet. Here, we show that the Spx proteins can also exert regulatory roles in the expression of additional virulence attributes of S. mutans. Competence activation is significantly impaired in Δspx strains and the production of mutacin IV and V is virtually abolished in ΔspxA1 strains. Unexpectedly, the ∆spxA2 strain showed increased production of glucans from sucrose, without affecting the total amount of bacteria within biofilms when compared with the parent strain. By using the rat caries model, we showed that the capacity of the ΔspxA1 and ΔspxA2 strains to cause caries on smooth tooth surfaces is significantly impaired. The ∆spxA2 strain also formed fewer lesions on sulcal surfaces. This report reveals that global regulation via Spx contributes to the cariogenic potential of S. mutans and highlights that animal models are essential in the characterization of bacterial traits implicated in virulence.
Fossilization of melanosomes via sulfurization
Authors: McNamara Maria E. , van Dongen Bart E. , Lockyer Nick P. , Bull Ian D. , Orr Patrick J. 
Published: April 2016

AbstractFossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur‐bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur‐rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py‐GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF‐SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non‐sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur‐rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.
Endothermic mosasaurs? Possible thermoregulation of Late Cretaceous mosasaurs (Reptilia, Squamata) indicated by stable oxygen isotopes in fossil bioapatite in comparison with coeval marine fish and pelagic seabirds
Authors: Harrell T. Lynn , Pérez‐Huerta Alberto , Suarez Celina A. 
Published: April 2016

AbstractThe thermoregulatory style of Late Cretaceous mosasaurs has become a highly controversial subject in vertebrate palaeontology. These extinct marine reptiles have previously been described as poikilothermic, endothermic or gigantothermic. Here we analyse three genera of mosasaurs from the Mooreville Chalk in Alabama (USA) of differing body mass, and compare their δ18OPO4 derived body temperatures (Tb) with those of coeval poikilothermic fish (Enchodus) and endothermic pelagic seabirds (Ichthyornis). Results show that all mosasaurs, Clidastes (Tb = 33.1°C), Platecarpus (Tb = 36.3°C), and Tylosaurus (Tb = 34.3°C), had elevated average body temperatures in relation to those of the fish (Tb = 28.3°C) and were closer to those of Ichthyornis (Tb = 38.6°C). The temperatures calculated for Enchodus compare well with previously reported temperature estimates for the Mooreville Chalk and the Tb of Ichthyornis compares well with temperatures that have been reported for modern seabirds, suggesting that this method provides accurate results. Finally, although there are small differences of body temperature among mosasaur genera, these are independent of size, and thus inferred body mass, suggesting that mosasaurs were not gigantotherms, but rather endotherms.
Microarray and genetic analysis reveals that csa‐miR159b plays a critical role in abscisic acid‐mediated heat tolerance in grafted cucumber plants
Authors: Li Hao , Wang Yu , Wang Ze , Guo Xie , Wang Feng , Xia Xiao‐Jian , Zhou Jie , Shi Kai , Yu Jing‐Quan , Zhou Yan‐Hong 
Published: April 2016

AbstractRoot‐shoot communication plays a vital role in plant growth, development and adaptation to environmental stimuli. Grafting‐induced stress tolerance is associated with the induction of plentiful stress‐related genes and proteins; the mechanism involved, however, remains obscure. Here, we show that the enhanced tolerance against heat stress in cucumber plants with luffa as rootstock was accompanied with an increased accumulation of abscisic acid (ABA), down‐regulation of a subset of microRNAs (miRNAs) but up‐regulation of their target genes and CsHSP70 accumulation in the shoots. Significantly, luffa rootstock and foliar application of ABA both down‐regulated csa‐miR159b and up‐regulated its target mRNAs CsGAMYB1 and CsMYB29‐like and CsHSP70 accumulation in cucumber, while ectopic expression of csa‐miR159b led to decreased heat tolerance, AtMYB33 transcript and AtHSP70 accumulation in Arabidopsis plants. Taken together, our results suggest that root‐originated signals such as ABA could alter miRNAs in the shoots, which have a major role in the post‐transcriptional regulation of the stress‐responsive genes.
Acclimation of the crucifer Eutrema salsugineum to phosphate limitation is associated with constitutively high expression of phosphate‐starvation genes
Authors: Velasco Vera Marjorie Elauria , Mansbridge John , Bremner Samantha , Carruthers Kimberley , Summers Peter S. , Sung Wilson W.L. , Champigny Marc J. , Weretilnyk Elizabeth A. 
Published: April 2016

AbstractEutrema salsugineum, a halophytic relative of Arabidopsis thaliana, was subjected to varying phosphate (Pi) treatments. Arabidopsis seedlings grown on 0.05 mm Pi displayed shortened primary roots, higher lateral root density and reduced shoot biomass allocation relative to those on 0.5 mm Pi, whereas Eutrema seedlings showed no difference in lateral root density and shoot biomass allocation. While a low Fe concentration mitigated the Pi deficiency response for Arabidopsis, Eutrema root architecture was unaltered, but adding NaCl increased Eutrema lateral root density almost 2‐fold. Eutrema and Arabidopsis plants grown on soil without added Pi for 4 weeks had low shoot and root Pi content. Pi‐deprived, soil‐grown Arabidopsis plants were stunted with senescing older leaves, whereas Eutrema plants were visually indistinguishable from 2.5 mm Pi‐supplemented plants. Genes associated with Pi starvation were analysed by RT‐qPCR. EsIPS2, EsPHT1;4 and EsPAP17 showed up‐regulated expression in Pi‐deprived Eutrema plants, while EsPHR1, EsWRKY75 and EsRNS1 showed no induction. Absolute quantification of transcripts indicated that PHR1, WRKY75 and RNS1 were expressed at higher levels in Eutrema plants relative to those in Arabidopsis regardless of external Pi. The low phenotypic plasticity Eutrema displays to Pi supply is consistent with adaptation to chronic Pi deprivation in its extreme natural habitat.
Diagnostic and prognostic factors for acute encephalopathy
Authors: Motojima Yukiko , Nagura Michiaki , Asano Yoshitaka , Arakawa Hiroshi , Takada Eiko , Sakurai Yoshio , Moriwaki Koichi , Tamura Masanori 
Published: April 2016

AbstractBackgroundAcute encephalopathy has the possibility of sequelae. While early treatment is required to prevent the development of sequelae, differential diagnosis is of the utmost priority. The aim of this study was therefore to identify parameters that can facilitate early diagnosis and prediction of outcome of acute encephalopathy.MethodsWe reviewed the medical charts of inpatients from 2005 to 2011 and identified 33 patients with febrile status epilepticus. Subjects were classified into an acute encephalopathy group (n = 20) and a febrile convulsion group (n = 13), and the parameters serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), ammonia (NH3), cerebrospinal fluid (CSF) tau protein, and CSF interleukin‐6 compared between them. Furthermore, the relationship between each parameter and prognosis was investigated in the encephalopathy group.ResultsSignificant differences in serum AST, ALT, and LDH were observed between the febrile convulsion and acute encephalopathy group. Moreover, a significant difference in serum LDH was noted between the patients with and without developmental regression at the time of hospital discharge in the encephalopathy group. In particular, CSF tau protein was found to be highly likely to indicate progress, with CSF tau protein >1000 pg/dL associated with poor prognosis leading to developmental regression.ConclusionSerum AST, ALT and LDH may be related to early diagnosis and prognosis, and should be carefully investigated in patients with encephalopathy. CSF tau protein could also be used as an indicator of poor prognosis in acute encephalopathy.
Expanded criteria for retinopathy of prematurity screening in moderately preterm infants: Single‐center pilot study
Authors: Yum Sook Kyung , Moon Cheong‐Jun , Youn Young‐Ah , Lee Jung Hyun , Kim So Young , Sung In Kyung 
Published: April 2016

AbstractBackgroundWhile developed countries seek to lower the gestational age and birthweight parameters in retinopathy of prematurity (ROP) screening, older, larger infants still develop ROP in other parts of the world. The aim of this study was therefore to define criteria to identify potential ROP developers who are outliers of the common screening range.MethodsA retrospective medical record review was performed in 147 inborn moderately preterm infants admitted to the neonatal intensive care unit during the study period. Univariate and logistic regression analysis was carried out.ResultsForty‐two infants developed ROP. Gestational age (31.4 ± 1.1 vs 32.4 ± 1.0 weeks, P = 0.000) and birthweight (1607.7 ± 339.4 vs 1846.4 ± 317.2 g, P = 0.000) were lower in those who developed ROP. Respiratory distress syndrome (P = 0.026) and documented sepsis (P = 0.003) were significant comorbidities on univariate analysis. Inotrope need >72 h starting in the first week of life (P = 0.004; OR, 5.181) and more than three transfusions of packed red blood cells (P = 0.028; OR, 3.891) were also significant, both on univariate and multivariate analysis.ConclusionsIn moderately preterm infants, status should be evaluated in order to effectively select candidates for ROP screening without missing potential ROP developers.