bluuebunny/crossref_metadata_2025_split huggingface dataset:
A polyphasic approach to the delimitation of diatom species: a case study for the genusPinnularia(Bacillariophyta)
Authors: Kollár Jan , Pinseel Eveline , Vanormelingen Pieter , Poulíčková Aloisie , Souffreau Caroline , Dvořák Petr , Vyverman Wim 
Published: December 2018

Diatoms are one of the most abundant and arguably the most species‐rich group of protists. Diatom species delimitation has often been based exclusively on the recognition of morphological discontinuities without investigation of other lines of evidence. Even thoughDNAsequences and reproductive experiments have revealed several examples of (pseudo)cryptic diversity, our understanding of diatom species boundaries and diversity remains limited. The cosmopolitan pennate raphid diatom genusPinnulariarepresents one of the most taxon‐rich diatom genera. In this study, we focused on the delimitation of species in one of the major clades of the genus, thePinnularia subgibbagroup, based on 105 strains from a worldwide origin. We compared genetic distances between the sequences of seven molecular markers and selected the most variable pair, the mitochondrialcox1 and nuclear encodedLSU rDNA, to formulate a primary hypothesis on the species limits using three single‐locus automated species delimitation methods. We compared theDNA‐based primary hypotheses with morphology and with other available lines of evidence. The results indicate that our data set comprised 15 species of theP. subgibbagroup. The vast majority of these taxa have an uncertain taxonomic identity, suggesting that several may be unknown to science and/or members of (pseudo)cryptic species complexes within theP. subgibbagroup.
Role of soluble inflammatory mediators and different immune cell populations in early control of symptomatic acute hepatitis C virus infection
Authors: Hengst Julia , Klein Andreas L. , Lunemann Sebastian , Deterding Katja , Hardtke Svenja , Falk Christine S. , Manns Michael P. , Cornberg Markus , Schlaphoff Verena , Wedemeyer Heiner 
Published: December 2018

SummaryThe natural course of acute Hepatitis C Virus (aHCV) infection is highly heterogeneous, and only few biomarkers have been identified to reliably predict the outcome of infection. We analysed a large panel of soluble inflammatory mediators, immune cell frequencies and phenotypes using peripheral blood samples from 26 patients with symptomatic aHCV infection from a controlled randomized clinical trial (ISRCTN88729946, www.isrctn.com). We found that patients with a spontaneous early HCV control demonstrated a distinct expression pattern of various soluble immune mediators including IFNα and IL‐16. Immune cell phenotype and frequency differed between patients who cleared the viral infection early (n=13) and those who remained HCV RNA positive after 12 weeks of observation (n=13) with a reduced ratio of CD4+ T cells to NK cells in the non–early clearer. Further, correlation analyses of 50 cytokines and chemokines revealed more positive correlations in between the distinct cytokines, especially for IFNα and IL‐16, and between the cytokines and HCV RNA levels in spontaneous early clearer patients. Beyond that, in vitro stimulation of CD4+ T cells with IL‐16 reduced the susceptibility of these cells to killing by IFNα‐activated NK cells. These data indicate that the immune cell composition and cytokine pattern varies considerably in patients with symptomatic aHCV infection. NK cell–mediated killing of CD4+ T cells might affect early control of HCV infection.
Atrial fibrillation is highly prevalent yet undertreated in patients with biopsy‐proven nonalcoholic steatohepatitis
Authors: Whitsett Maureen , Wilcox Jane , Yang Amy , Zhao Lihui , Rinella Mary , VanWagner Lisa B. 
Published: December 2018

AbstractBackground & AimsNonalcoholic steatohepatitis (NASH) is associated with increased cardiovascular disease. Atrial fibrillation is a prominent risk marker for underlying cardiovascular disease with a prevalence of 2% in patients <65 years old. Atrial fibrillation prevalence in NASH is unknown. We sought to assess the prevalence and impact of atrial fibrillation on healthcare utilization in NASH.MethodsPatients were identified from a tertiary care centre Electronic Database from 2002 to 2015. International Classification of Diseases 9 (ICD9) codes identified comorbidities and atrial fibrillation. Descriptive statistics were used to compare characteristics between patients with NASH with and without atrial fibrillation.ResultsOf 9108 patients with ICD9 diagnosis of NASH, 215 (2.3%, mean age 57 years, 32% male) had biopsy‐proven NASH. Atrial fibrillation prevalence was 4.6%. Patients with NASH and atrial fibrillation had a higher prevalence of heart failure (54.5% vs 8.8%, P < 0.001) and cerebrovascular (27.3% vs 2.0%, P < 0.001) or vascular disease (54.5% vs 13.2%, P = 0.002), compared to NASH without atrial fibrillation. All patients with NASH and atrial fibrillation had a CHA2DS2VASc score ≥2 indicating high stroke risk and need for anticoagulation. Eight of 10 patients were eligible for anticoagulation and 5 of 8 (62.5%) received appropriate therapy.ConclusionAtrial fibrillation prevalence is two‐fold higher in patients with NASH compared to the general population. Patients with NASH have a high risk of stroke; however, many do not receive appropriate guideline‐directed therapy. Future studies are needed to identify whether guideline‐based management of atrial fibrillation in NASH reduces cardiovascular morbidity and mortality.
Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus
Authors: Herrou Julien , Willett Jonathan W. , Fiebig Aretha , Varesio Lydia M. , Czyż Daniel M. , Cheng Jason X. , Ultee Eveline , Briegel Ariane , Bigelow Lance , Babnigg Gyorgy , Kim Youngchang , Crosson Sean 
Published: December 2018

SummaryMolecular components of the Brucella abortus cell envelope play a major role in its ability to infect, colonize and survive inside mammalian host cells. In this study, we have defined a role for a conserved gene of unknown function in B. abortus envelope stress resistance and infection. Expression of this gene, which we name eipA, is directly activated by the essential cell cycle regulator, CtrA. eipA encodes a soluble periplasmic protein that adopts an unusual eight‐stranded β‐barrel fold. Deletion of eipA attenuates replication and survival in macrophage and mouse infection models, and results in sensitivity to treatments that compromise the cell envelope integrity. Transposon disruption of genes required for LPS O‐polysaccharide biosynthesis is synthetically lethal with eipA deletion. This genetic connection between O‐polysaccharide and eipA is corroborated by our discovery that eipA is essential in Brucella ovis, a naturally rough species that harbors mutations in several genes required for O‐polysaccharide production. Conditional depletion of eipA expression in B. ovis results in a cell chaining phenotype, providing evidence that eipA directly or indirectly influences cell division in Brucella. We conclude that EipA is a molecular determinant of Brucella virulence that functions to maintain cell envelope integrity and influences cell division.
Fungicide resistance toward fludioxonil conferred by overexpression of the phosphatase gene MoPTP2 inMagnaporthe oryzae
Authors: Bohnert Stefan , Heck Larissa , Gruber Christoph , Neumann Hendrik , Distler Ute , Tenzer Stefan , Yemelin Alexander , Thines Eckhard , Jacob Stefan 
Published: December 2018

SummaryThe fungicide fludioxonil causes hyperactivation of the Hog1p MAPK within the high‐osmolarity glycerol signaling pathway essential for osmoregulation in pathogenic fungi. The molecular regulation of MoHog1p phosphorylation is not completely understood in pathogenic fungi. Thus, we identified and characterized the putative MoHog1p‐interacting phosphatase geneMoPTP2in the filamentous rice pathogenMagnaporthe oryzae. We found overexpression ofMoPTP2conferred fludioxonil resistance inM. oryzae, whereas the ‘loss of function’ mutantΔMoptp2was more susceptible toward the fungicide. Additionally, quantitative phosphoproteome profiling of MoHog1p phosphorylation revealed lower phosphorylation levels of MoHog1p in the MoPtp2p overexpression mutant compared to the wild‐type strain, whereas MoHog1p phosphorylation increased in theΔMoptp2mutant. Furthermore, we identified a set of MoHog1p‐dependent genes regulated by the MoPtp2p expression level. Our results indicate that the phosphatase MoPtp2p is involved in the regulation of MoHog1p phosphorylation and that overexpression of the geneMoPTP2is a novel molecular mechanism of fungicide resistance.
The UzcRS two‐component system in Caulobacter crescentus integrates regulatory input from diverse auxiliary regulators
Authors: Park Dan M. , Overton K. Wesley , Jiao Yongqin 
Published: December 2018

SummaryThe UzcRS two‐component system in Caulobacter crescentus mediates widespread transcriptional activation in response to the metals U, Zn and Cu. Unexpectedly, a screen for mutations that affected the activity of the UzcR‐regulated urcA promoter (PurcA) revealed four previously uncharacterized proteins whose inactivation led to metal‐independent induction of PurcA. Using molecular genetics and functional genomics, we find that these auxiliary regulators control PurcA expression by modulating the activity of UzcRS through distinct mechanisms. An ABC transporter with a periplasmic metallo‐aminopeptidase domain forms a sensory complex with UzcRS, antagonizing metal dependent stimulation by virtue of its ATPase and peptidase domains. Two MarR‐like transcription factors synergistically regulate UzcRS activity by repressing the expression of the membrane proteins UzcY and UzcZ, which stimulate UzcRS activity and enhance its sensitivity to a more environmentally relevant U/Zn/Cu concentration range. Additionally, the membrane protein UzcX, whose expression is positively regulated by UzcR, provides a mechanism of feedback inhibition within the UzcRS circuit. Collectively, these data suggest that UzcRS functions as the core‐signaling unit within a multicomponent signal transduction pathway that includes a diverse set of auxiliary regulators, providing further insight into the complexity of signaling networks.
Activation of immune receptor Rx1 triggers distinct immune responses culminating in cell death after 4 hours
Authors: Knip Marijn , Richard Manon M.S. , Oskam Lisa , van Engelen Hylco T.D. , Aalders Thomas , Takken Frank L.W. 
Published: December 2018

SummaryIntracellular nucleotide‐binding leucine‐rich repeat (NLR)‐type immune receptors are a fundamental part of plant immune systems. As infection occurs at foci, activation of immune responses is typically non‐uniform and non‐synchronized, hampering the systematic dissection of their cellular effects and determining their phasing. We investigated the potato NLR Rx1 using the CESSNA (Controlled Expression of effectors for Synchronized and Systemic NLR Activation) platform. CESSNA‐mediated Potato virus X coat protein (CP) expression allowed the monitoring of Rx1‐mediated immune responses in a quantitative and reproducible manner. Rx1 was found to trigger a reactive oxygen species (ROS) burst and ion leakage within 1 h and a change in autofluorescence within 2 h after the induction of CP production. After 2 h, HIN1 expression was increased and single‐stranded DNA (ssDNA) damage and loss of cellular integrity became apparent, followed by double‐stranded DNA (dsDNA) damage after 3 h and increased PR‐1a, LOX, ERF1 and AOX1B expression and cell death at 4 h. Nuclear exclusion of Rx1 resulted in increased basal levels of ROS and permitted Rx1 activation by an Rx1‐breaking CP variant. In contrast, nuclear‐targeted Rx1 showed diminished basal ROS levels, and only avirulent CP could trigger a compromised ROS production. Both nuclear‐excluded and nuclear‐targeted Rx1 triggered a delayed ion leakage compared with non‐modified Rx1, suggesting that ion leakage and ROS production originate from distinct signalling pathways. This work offers novel insights into the influence of Rx1 localization on its activity, and the interplay between Rx1‐triggered processes.
The histone‐like protein HupB influences biofilm formation and virulence in Xanthomonas citri ssp. citri through the regulation of flagellar biosynthesis
Authors: Conforte Valeria P. , Malamud Florencia , Yaryura Pablo M. , Toum Terrones Laila , Torres Pablo S. , De Pino Verónica , Chazarreta Cristian N. , Gudesblat Gustavo E. , Castagnaro Atilio P. , R. Marano María , Vojnov Adrian A. 
Published: December 2018

SummaryCitrus canker is an important disease of citrus, whose causal agent is the bacterium Xanthomonas citri ssp. citri (Xcc). In previous studies, we found a group of Xcc mutants, generated by the insertion of the Tn5 transposon, which showed impaired ability to attach to an abiotic substrate. One of these mutants carries the Tn5 insertion in hupB, a gene encoding a bacterial histone‐like protein, homologue to the β‐subunit of the Heat‐Unstable (HU) nucleoid protein of Escherichia coli. These types of protein are necessary to maintain the bacterial nucleoid organization and the global regulation of gene expression. Here, we characterized the influence of the mutation in hupB regarding Xcc biofilm formation and virulence. The mutant strain hupB was incapable of swimming in soft agar, whereas its complemented strain partially recovered this phenotype. Electron microscope imaging revealed that impaired motility of hupB was a consequence of the absence of the flagellum. Comparison of the expression of flagellar genes between the wild‐type strain and hupB showed that the mutant exhibited decreased expression of fliC (encoding flagellin). The hupB mutant also displayed reduced virulence compared with the wild‐type strain when they were used to infect Citrus lemon plants using different infection methods. Our results therefore show that the histone‐like protein HupB plays an essential role in the pathogenesis of Xcc through the regulation of biofilm formation and biosynthesis of the flagellum.
Association of klotho gene polymorphism and the regulation of calcium‐phosphate metabolism disorders in patients with end‐stage renal disease
Authors: Zeng Qing‐Ya , Xia Zhi‐Yin , Tong Yan‐Shan , Sun Liang , Mou Hong‐Bin , Chen Rui , Bi Guang‐Yu , Liu Chang‐Hua 
Published: December 2018

ABSTRACTBackgroundKlotho G‐395‐A gene polymorphism is associated with several diseases; however, its association with calcium‐phosphate metabolism disorders in end‐stage renal disease (ESRD) is unknown.MethodsA total of 137 patients with ESRD and 80 healthy adults (control) were enrolled in the study. Patients with ESRD were divided into three subgroups: haemodialysis (A1, n = 52), peritoneal dialysis (A2, n = 30), and non‐dialysis (A3, n = 55). The klotho G‐395‐A genotype was detected by TaqMan PCR assay, and ELISA was used to detect the soluble klotho protein (sKL) and fibroblast growth factor (FGF23). Intact parathyroid hormone (iPTH) and other related clinical biochemical parameters were also analyzed for all subjects.Results(i) Three genotypes (GG, GA and AA) of KL G‐395A were detected, and a significant difference between the ESRD and control groups was observed, (ii) sKL was inversely associated with FGF23 in each subgroup and phosphate and positively associated with calcium in A1 and A3. FGF23 was positively associated with phosphate and inversely associated with calcium in each subgroup, (iii) a statistical difference in levels of sKL and FGF23 was observed between GG and AA, as well as between GA and AA. The expression of sKL was lowest and the level of FGF23 was highest in AA and (iv). GA + AA genotypes and FGF23 were risk factors and sKL might be protective factor of calcium‐phosphate metabolism disorders.ConclusionSoluble klotho protein and FGF23 were associated with the regulation of calcium and phosphate metabolism, and the A allele of the G‐395A klotho gene polymorphism could be a risk factor on calcium‐phosphate metabolism disorders in patients with ESRD.
Acute cellular rejection treatment outcomes stratified by Banff grade in pediatric kidney transplant
Authors: Chen Justin , Liverman Rochelle , Garro Rouba , Jernigan Stephanie , Travers Curtis , Winterberg Pamela D. 
Published: December 2018

AbstractIntroductionThere are limited data to guide optimal treatment strategies for acute cellular rejection (ACR) based on Banff grade for pediatric kidney transplant recipients. This report reviews a large pediatric transplant center's experience with ACR.Materials and MethodsA retrospective analysis of pediatric kidney transplant recipients at our center from 2007 to 2014 was performed. Primary outcomes were incidence of graft failure and graft function one year following ACR based on Banff grade and treatment received.ResultsA total of 204 patients were reviewed, of which 65 received rejection treatment with either an oral steroid cycle (n = 16), intravenous steroid pulse (n = 28), or anti‐thymocyte globulin (rATG, n = 21). Overall, patients received rATG for treatment of more severe rejection associated with impaired graft function and as a group experienced statistically significant improvements in eGFR over the year following treatment, though most did not regain baseline graft function.DiscussionOur data suggest that rATG is partially effective in treating ACR, but our study was underpowered to determine the effect of different treatments based on Banff grade. Since there is limited literature to guide clinical treatment of ACR in children, large transplant centers should collaborate to evaluate outcomes and establish evidence‐based practice.
Heart transplantation in two adolescents with Danon disease
Authors: Oren Daniel , Chau Peter , Manning Melanie , Kwong Joann , Kaufman Beth D. , Maeda Katsuhide , Rosenthal David N. , Hollander Seth A. 
Published: December 2018

AbstractDanon disease (DD) is an X‐linked dominant disorder caused by a mutation in the lysosomal‐associated membrane protein‐2 (LAMP‐2) gene coding for the LAMP‐2 protein. We report two cases of successful heart transplantation (HT) in adolescent brothers with DD, including one who was bridged to HT for 34 days with a HeartWare left ventricular assist device. In both patients, the post‐transplant course was complicated by profound skeletal muscle weakness that resolved with corticosteroid withdrawal. These cases highlight that both HT and ventricular assist device support are feasible in patients with DD. Corticosteroid use may exacerbate skeletal myopathy, and therefore, steroid minimization may be warranted whenever possible.
Potassium deficiency aggravates yield loss in rice by restricting the translocation of non‐structural carbohydrates under Sarocladium oryzae infection condition
Authors: Zhang Jianglin , Lu Zhifeng , Pan Yonghui , Ren Tao , Cong Rihuan , Lu Jianwei , Li Xiaokun 
Published: December 2018

Sheath rot disease (ShR) caused by Sarocladium oryzae (S. oryzae) infection is an emerging disease that causes severe yield loss by restricting the translocation of non‐structural carbohydrates (NSC). Potassium (K) nutrition plays a critical role in disease resistance and the exportation of NSC. However, the physiological mechanisms of K with respect to ShR have not been thoroughly elucidated to date. The objectives of this study were to reveal the mechanisms by which K increases ShR resistance by regulating NSC translocation of rice, therefore, a field experiment combined with an inoculation experiment was conducted. We demonstrate that ShR disease incidence and disease index decreased dramatically with an increasing K application. K deficiency sharply induced the accumulation of NSC in the flag leaf (FL) and flag leaf sheath (FLS) under S. oryzae infection condition, which reduced the contribution of transferred NSC to final yield. A permutational multivariate analysis showed that K deficiency had a greater (49.0%, P < 0.001) effect on the NSC content variation in FL than that of S. oryzae infection (15.0%, P < 0.001). S. oryzae infection dramatically increased the difference in apparent transferred mass of NSC and cell membrane injury of diseased organs between K‐deficient and K‐sufficient rice. Finally, we demonstrate that cell membrane injury was a limiting factor imposed by K deficiency, which restricts the export of NSC from source organs. This work highlights the importance of K in improving ShR resistance by regulating NSC translocation (particularly the stem NSC).
Preservation of boar semen: An update
Authors: Pezo Felipe , Romero Fernando , Zambrano Fabiola , Sánchez Raúl Segundo 
Published: December 2018

ContentsIn the pork industry, artificial insemination and the storage of boar semen in liquid at 17°C are routinely applied to optimize the ejaculate and bring about rapid genetic changes that are reflected in the animal protein. Although the results are satisfactory, they are below what occurs with natural mating. It is currently possible to preserve boar semen with storage at 17°C and slow freezing, since to date there is only one study on vitrification, with negative results applicable only in the case of implementing an intracytoplasmic sperm injection. In both methods and due to the sensitivity of boar sperm to osmotic and temperature changes, there is a loss in the quality of the initial sample; however, slow freezing in boar semen has greater deleterious effects on the sample that are reflected in the pregnancy rates and number of live births. Therefore, only 1% of all inseminations are done with frozen semen. The aim of this review is to provide advances and results of studies conducted on the preservation of boar semen, delving more deeply into the critical points that each of the preservation techniques presents, including bacterial contamination, extender components, temperature, ice nucleation, use of additives in extenders and the main deleterious effects on sperm quality.
Mitochondrial function modulates touch signalling in Arabidopsis thaliana
Authors: Xu Yue , Berkowitz Oliver , Narsai Reena , De Clercq Inge , Hooi Michelle , Bulone Vincent , Van Breusegem Frank , Whelan James , Wang Yan 
Published: December 2018

SummaryPlants respond to short‐ and long‐term mechanical stimuli, via altered transcript abundance and growth respectively. Jasmonate, gibberellic acid and calcium have been implicated in mediating responses to mechanical stimuli. Previously it has been shown that the transcript abundance for the outer mitochondrial membrane protein of 66 kDa (OM66), is induced several fold after 30 min in response to touch. Therefore, the effect of mitochondrial function on the response to mechanical stimulation by touch at 30 min was investigated. Twenty‐five mutants targeting mitochondrial function or regulators revealed that all affected the touch transcriptome. Double and triple mutants revealed synergistic or antagonistic effects following the observed responses in the single mutants. Changes in the touch‐responsive transcriptome were localised, recurring with repeated rounds of stimulus. The gene expression kinetics after repeated touch were complex, displaying five distinct patterns. These transcriptomic responses were altered by some regulators of mitochondrial retrograde signalling, such as cyclic dependent protein kinase E1, a kinase protein in the mediator complex, and KIN10 (SnRK1 − sucrose non‐fermenting related protein kinase 1), revealing an overlap between the touch response and mitochondrial stress signalling and alternative mitochondrial metabolic pathways. Regulatory network analyses revealed touch‐induced stress responses and suppressed growth and biosynthetic processes. Interaction with the phytohormone signalling pathways indicated that ethylene and gibberellic acid had the greatest effect. Hormone measurements revealed that mutations of genes that encoded mitochondrial proteins altered hormone concentrations. Mitochondrial function modulates touch‐induced changes in gene expression directly through altered regulatory networks, and indirectly via altering hormonal levels.