julilili42/papers huggingface dataset:
Functionally Redundant RXLR Effectors from Phytophthora infestans Act at Different Steps to Suppress Early flg22-Triggered Immunity
2014-04-24

Genome sequences of several economically important phytopathogenic oomycetes have revealed the presence of large families of so-called RXLR effectors. Functional screens have identified RXLR effector repertoires that either compromise or induce plant defense responses. However, limited information is available about the molecular mechanisms underlying the modes of action of these effectors in planta. The perception of highly conserved pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs), such as flg22, triggers converging signaling pathways recruiting MAP kinase cascades and inducing transcriptional re-programming, yielding a generic anti-microbial response. We used a highly synchronizable, pathogen-free protoplast-based assay to identify a set of RXLR effectors from Phytophthora infestans (PiRXLRs), the causal agent of potato and tomato light blight that manipulate early stages of flg22-triggered signaling. Of thirty-three tested PiRXLR effector candidates, eight, called Suppressor of early Flg22-induced Immune response (SFI), significantly suppressed flg22-dependent activation of a reporter gene under control of a typical MAMP-inducible promoter (pFRK1-Luc) in tomato protoplasts. We extended our analysis to Arabidopsis thaliana, a non-host plant species of P. infestans. From the aforementioned eight SFI effectors, three appeared to share similar functions in both Arabidopsis and tomato by suppressing transcriptional activation of flg22-induced marker genes downstream of post-translational MAP kinase activation. A further three effectors interfere with MAMP signaling at, or upstream of, the MAP kinase cascade in tomato, but not in Arabidopsis. Transient expression of the SFI effectors in Nicotiana benthamiana enhances susceptibility to P. infestans and, for the most potent effector, SFI1, nuclear localization is required for both suppression of MAMP signaling and virulence function. The present study provides a framework to decipher the molecular mechanisms underlying the manipulation of host MAMP-triggered immunity (MTI) by P. infestans and to understand the basis of host versus non-host resistance in plants towards P. infestans.
Mining Herbaria for Plant Pathogen Genomes: Back to the Future
2014-04-24

Since the dawn of agriculture, plant pathogens and pests have been a scourge of humanity. Yet we have come a long way since the Romans attempted to mitigate the effects of plant disease by worshipping and honoring the god Robigus [1]. Books in the Middle Ages by Islamic and European scholars described various plant diseases and even proposed particular disease management strategies [1]. Surprisingly, the causes of plant diseases remained a matter of debate over a long period. It took Henri-Louis Duhamel du Monceau's elegant demonstration in his 1728 “Explication Physique” paper that a “contagious” fungus was responsible for a saffron crocus disease to usher in an era of documented scientific inquiry [2]. Confusion and debate about the exact nature of the causal agents of plant diseases continued until the 19th century, which not only saw the first detailed analyses of plant pathogens but also provided much-needed insight into the mechanisms of plant disease. An example of this is Anton de Bary's demonstration that a “fungus” is a cause, not a consequence, of plant disease [3]. This coming of age of plant pathology was timely. In the 19th century, severe plant disease epidemics hit Europe and caused economic and social upheaval. These epidemics were not only widely covered in the press but also recognized as serious political issues by governments [1], [4]–[6]. Many of the diseases, including late blight of potato, powdery and downy mildew of grapevine, as well as phylloxera, were due to exotic introductions from the Americas and elsewhere. These and subsequent epidemics motivated scientific investigations into crop breeding and plant disease management that developed into modern plant pathology science over the 20th century. Nowadays, our understanding of plant pathogens and the diseases they cause greatly benefits from molecular genetics and genomics. All aspects of plant pathology, from population biology and epidemiology to mechanistic research, are impacted. The polymerase chain reaction (PCR) first enabled access to plant pathogen DNA sequences from historical specimens deposited in herbaria [7]–[9]. Historical records in combination with herbarium specimens have turned out to provide powerful tools for understanding the course of past plant epidemics. Recently, thanks to new developments in DNA sequencing technology, it has become possible to reconstruct the genomes of plant pathogens in herbaria [10], [11]. In this article, we first summarize how whole genome analysis of ancient DNA has been recently used to reconstruct the 19th-century potato-blight epidemic that rapidly spread throughout Europe and triggered the Irish potato famine. We then discuss the exciting prospects offered by the emergence of the discipline of ancient plant pathogen genomics.
Model-Based Investigations of Different Vector-Related Intervention Strategies to Eliminate Visceral Leishmaniasis on the Indian Subcontinent
2014-04-24

The elimination of infectious diseases requires reducing transmission below a certain threshold. The Visceral Leishmaniasis (VL) Elimination Initiative in Southeast Asia aims to reduce the annual VL incidence rate below 1 case per 10,000 inhabitants in endemic areas by 2015 via a combination of case management and vector control. Using a previously developed VL transmission model, we investigated transmission thresholds dependent on measures reducing the sand fly density either by killing sand flies (e.g., indoor residual spraying and long-lasting insecticidal nets) or by destroying breeding sites (e.g., environmental management). Model simulations suggest that elimination of VL is possible if the sand fly density can be reduced by 67% through killing sand flies, or if the number of breeding sites can be reduced by more than 79% through measures of environmental management. These results were compared to data from two recent cluster randomised controlled trials conducted in India, Nepal and Bangladesh showing a 72% reduction in sand fly density after indoor residual spraying, a 44% and 25% reduction through the use of long-lasting insecticidal nets and a 42% reduction after environmental management. Based on model predictions, we identified the parameters within the transmission cycle of VL that predominantly determine the prospects of intervention success. We suggest further research to refine model-based predictions into the elimination of VL.
Cortisol increases CXCR4 expression but does not affect CD62L and CCR7 levels on specific T cell subsets in humans
2014-04-24

Glucocorticoids are well known to affect T cell migration, leading to a redistribution of the cells from blood to the bone marrow, accompanied by a concurrent suppression of lymph node homing. Despite numerous studies in this context, with most of them employing synthetic glucocorticoids in nonphysiological doses, the mechanisms of this redistribution are not well understood. Here, we investigated in healthy men the impact of cortisol at physiological concentrations on the expression of different migration molecules on eight T cell subpopulations in vivo and in vitro. Hydrocortisone (cortisol, 22 mg) infused during nocturnal rest when endogenous cortisol levels are low, compared with placebo, differentially reduced numbers of T cell subsets, with naive CD4 + and CD8 + subsets exhibiting the strongest reduction. Hydrocortisone in vivo and in vitro increased CXCR4 expression, which presumably mediates the recruitment of T cells to the bone marrow. Expression of the lymph node homing receptor CD62L on total CD3 + and CD8 + T cells appeared reduced following hydrocortisone infusion. However, this was due to a selective extravasation of CD62L + T cell subsets, as hydrocortisone affected neither CD62L expression on a subpopulation level nor CD62L expression in vitro. Corresponding results in the opposite direction were observed after blocking of endogenous cortisol synthesis by metyrapone. CCR7, another lymph node homing receptor, was also unaffected by hydrocortisone in vitro. Thus, cortisol seems to redirect T cells to the bone marrow by upregulating their CXCR4 expression, whereas its inhibiting effect on T cell homing to lymph nodes is apparently regulated independently of the expression of classical homing receptors.
Silylamide Complexes of Chromium(II), Manganese(II), and Cobalt(II) Bearing the Ligands N(SiHMe2)2 and N(SiPhMe2)2
2014-04-24

Bis(dimethylsilyl)amide and bis(dimethylphenylsilyl)amide complexes of the divalent transition metals chromium, manganese, and cobalt were synthesized. Dimeric, donor-free {Mn[N(SiHMe2)2]2}2 could be obtained via two different pathways, a salt metathesis route (utilizing MnCl2(thf)1.5 and LiN(SiHMe2)2) and a transsilylamination protocol (utilizing Mn[N(SiMe3)2]2(thf) and HN(SiHMe2)2). Addition of 1,1,3,3-tetramethylethylendiamine (tmeda) to {Mn[N(SiHMe2)2]2}2 yielded the monomeric adduct Mn[N(SiHMe2)2]2(tmeda). The syntheses of Cr[N(SiHMe2)2]2(tmeda), Co[N(SiMe3)2][N(SiHMe2)2](tmeda), and Co[N(SiHMe2)2]2(tmeda) were achieved by transsilylamination from Cr[N(SiMe3)2]2(tmeda) and {Co[N(SiMe3)2]2}2(μ-tmeda), respectively. Bis(dimethylphenylsilyl)amide complexes Mn[N(SiMe2Ph)2]2, Cr[N(SiMe2Ph)2]2, and Co[N(SiMe2Ph)2]2(thf) were obtained via salt metathesis employing MCl2(thf)x (M = Cr, Mn, Co) with equimolar amounts of LiN(SiMe2Ph)2 in n-hexane. Treatment of CrCl2 with LiN(SiMe2Ph)2 in thf gave Cr[N(SiMe2Ph)2]2(thf)2, featuring an almost square planar trans-coordination. All complexes were examined by elemental analyses, DRIFT and UV-vis spectroscopy, as well as X-ray structure analysis, paying particular attention to secondary M---SiH β-agostic and M---π(arene) interactions. Magnetic moments were determined by Evans' method.
No Migration in a Realistic Utopia? Rawls's The Law of Peoples and the Topic of Migration
2014-04-24

The current debate on migration and ethics is to a high extend informed by Rawlsian thinking. The ideas Rawls himself has put forward on this topic, however, are rarely discussed. One reason for that is Rawls’s explicit exclusion of all questions related to migratory movements in his work The Law of Peoples. In this paper I argue that it is still valuable to examine this work on the foreign relations of liberal democracies more closely, especially if one is concerned with the moral and ethical challenges migration brings about: I will show that Rawls brings forward substantial arguments on these matters. The paper is divided into three sections. After a first introductory part I will discuss Rawls’s ideas on migration in more detail. In the concluding part of my paper, I will summarize my findings and present some more general considerations on the implications my discussion of The Law of Peoples might have.
‘Baroque Spain’ As Metaphor.Hispanidad, Europeanism and Cold War Anti-Communism in Francoist Spain
2014-04-25

The Franco regime's notion of hispanidad stood for a specific style of thought, based upon the imagery of 'Baroque Spain' and referring to the sense of cultural superiority and religious mission as well as to the close relations between Spain and 'Hispanoamérica'. Using references to Baroque arts and architecture as a rhetorical instrument, the discourse of hispanidad was meant to strengthen the assertion of an essential unity between Spain and its former colonies. To assert themselves within the regime, Spanish politicians had to adapt their purposes to this discourse. Surprisingly, this principle applied also to the cautious European policy of the early 1950s as well as to the regime's aggressive Cold War anti-communism. The ideological flexibility of this concept of hispanidad is shown by the example of the Centro Europeo de Documentación e Información (CEDI). The CEDI was founded in 1952 with the active support of the Instituto de Cultura Hispánica (ICH) as a political instrument, but gradually turned into an independent platform for conservative European elites, transgressing the role it had originally been assigned within the Franco regime.
CoPc and CoPcF16 on gold: Site-specific charge-transfer processes
2014-04-25

Interface properties of cobalt(II) phthalocyanine (CoPc) and cobalt(II) hexadecafluoro-phthalocyanine (CoPcF 16 ) to gold are investigated by photo-excited electron spectroscopies (X-ray photoemission spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS) and X-ray excited Auger electron spectroscopy (XAES)). It is shown that a bidirectional charge transfer determines the interface energetics for CoPc and CoPcF 16 on Au. Combined XPS and XAES measurements allow for the separation of chemical shifts based on different local charges at the considered atom caused by polarization effects. This facilitates a detailed discussion of energetic shifts of core level spectra. The data allow the discussion of site-specific charge-transfer processes.
CD40-independent natural killer-cell help promotes dendritic cell vaccine-induced T-cell immunity against endogenous B-cell lymphoma
2014-04-26

It is well established that an interplay between natural killer (NK) cells and dendritic cells (DCs) gives rise to their reciprocal activation and provides a Th1-biased cytokine milieu that fosters antitumor T-cell responses. Ex vivo-differentiated DCs transferred into mice strongly stimulate endogenous NK cells to produce interferon (IFN)-γ and initiate a cascade that eventually leads to cytotoxic T-lymphocyte responses. We show that the ability of exogenous DCs to trigger this pathway obviates CD40 signaling and CD4(+) T-cell help and depends on a preceding maturation step. Importantly, this mechanism was also effective in endogenously arising tumors where IFN-γ production is compromised in contrast to transplantable tumors. In c-myc-transgenic mice developing spontaneous lymphomas, injection of unpulsed DCs caused NK-cell activation and induced CD8(+) T cells capable of recognizing the lymphoma cells. Animals treated with unpulsed DCs showed a survival benefit compared to untreated myc mice. Hence, tumor immunity induced by DC-based vaccines not only depends on specific antigens loaded on the DCs. Rather, DC vaccines generate broader immune responses, because endogenous DCs presenting tumor antigens may also become stimulated by NK cells that were activated by exogenous DCs. Thus, the DC/NK-cell/cytotoxic T lymphocyte axis may commonly have relevance for DC-based vaccination protocols in clinical settings.
A forager–herder trade-off, from broad-spectrum hunting to sheep management at Aşıklı Höyük, Turkey
2014-04-28

Significance This article provides original results on the formative conditions of sheep domestication in the Near East. To our knowledge, none of the results has been published before, and the results are expected to be of wide interest to archaeologists, biologists, and other professionals interested in evolutionary and cultural processes of animal domestication.
Communication: Radial distribution functions in a two-dimensional binary colloidal hard sphere system
2014-04-28

Two-dimensional hard disks are a fundamentally important many-body model system in classical statistical mechanics. Despite their significance, a comprehensive experimental data set for two-dimensional single component and binary hard disks is lacking. Here, we present a direct comparison between the full set of radial distribution functions and the contact values of a two-dimensional binary colloidal hard sphere model system and those calculated using fundamental measure theory. We find excellent quantitative agreement between our experimental data and theoretical predictions for both single component and binary hard disk systems. Our results provide a unique and fully quantitative mapping between experiments and theory, which is crucial in establishing the fundamental link between structure and dynamics in simple liquids and glass forming systems.
Accelerometer-based quantitative analysis of axial nocturnal movements differentiates patients with Parkinson's disease, but not high-risk individuals, from controls
2014-04-28

Compared with controls, patients with PD had an overall decreased mean acceleration, as well as smaller and shorter nocturnal axial movements. These changes did not occur in our potential HR-PD individuals, suggesting that relevant axial movement alterations during sleep have either not developed or cannot be detected by the means applied in this at-risk cohort.
Development of Metal Cyanurates: The Example of Barium Cyanurate (BCY)
2014-04-28

Abstract Metal cyanurate compounds were prepared by means of solid‐state metathesis reactions between a metal halide and an alkali cyanurate. Following this procedure, a mixture of BaCl 2 and K(OCN) was heated in a fused silica tube at 575 °C to yield highly crystalline barium cyanurate. This reaction was analyzed by differential scanning calorimetry (DSC) measurements and involves a cyclotrimerization of cyanate ions to yield the cyclic cyanurate (O 3 C 3 N 3 ) 3– ion. The crystal structure of Ba 3 (O 3 C 3 N 3 ) 2 was refined by single‐crystal X‐ray diffraction, and the presence of cyanurate was verified by infrared spectroscopy.
Impact of anesthetics on 3'-[18F]fluoro-3'-deoxythymidine ([18F]FLT) uptake in animal models of cancer and inflammation.
2014-04-28

The aim of this study was to evaluate the impact of different anesthetics on 3'-[18F]fluoro-3'-deoxythymidine ([18F]FLT) uptake in carcinomas and arthritic ankles. To determine the amount of [18F]FLT uptake in subcutaneous CT26 colon carcinomas or arthritic ankles, spontaneously room air/medical air-breathing mice were anesthetized with isoflurane, a combination of medetomidine/midazolam, or ketamine/xylazine. Mice were kept conscious or anesthetized during [18F]FLT uptake before the 10-minute static positron emission tomographic (PET) investigations. [18F]FLT uptake in CT26 colon carcinomas and arthritic ankles was calculated by drawing regions of interest. We detected a significantly reduced (4.4 ± 0.9 %ID/cm3) [18F]FLT uptake in the carcinomas of ketamine/xylazine-anesthetized mice compared to the [18F]FLT-uptake in carcinomas of medetomidine/midazolam- (7.0 ± 1.5 %ID/cm3) or isoflurane-anesthetized mice (6.4 ± 1.5 %ID/cm3), whereas no significant differences were observed in arthritic ankles regardless of whether mice were anesthetized or conscious during tracer uptake. The time-activity curves of carcinomas and arthritic ankles yielded diverse [18F]FLT accumulation related to the used anesthetics. [18F]FLT uptake dynamics are different in arthritic ankles and carcinoma, and the magnitude and pharmacokinetics of [18F]FLT uptake are sensitive to anesthetics. Thus, for preclinical in vivo [18F]FLT PET studies in experimental tumor or inflammation models, we recommend the use of isoflurane anesthesia as it yields a stable tracer uptake and is easy to handle.
Confinement in Coulomb gauge
2014-04-28

We review our lattice results concerning the Gribov-Zwanziger confinement mechanism in Coulomb gauge.In particular, we verify the validity of Gribov's IR divergence condition for the Coulomb ghost form factor.We also show how the quark self energy is, like that of the transverse gluon, IR divergent, thus effectively extending the Gribov-Zwanziger scenario to full QCD.
Streptomyces-Induced Resistance Against Oak Powdery Mildew Involves Host Plant Responses in Defense, Photosynthesis, and Secondary Metabolism Pathways
2014-04-29

Rhizobacteria are known to induce defense responses in plants without causing disease symptoms, resulting in increased resistance to plant pathogens. This study investigated how Streptomyces sp. strain AcH 505 suppressed oak powdery mildew infection in pedunculate oak, by analyzing RNA-Seq data from singly- and co-inoculated oaks. We found that this Streptomyces strain elicited a systemic defense response in oak that was, in part, enhanced upon pathogen challenge. In addition to induction of the jasmonic acid/ethylene–dependent pathway, the RNA-Seq data suggests the participation of the salicylic acid–dependent pathway. Transcripts related to tryptophan, phenylalanine, and phenylpropanoid biosynthesis were enriched and phenylalanine ammonia lyase activity increased, indicating that priming by Streptomyces spp. in pedunculate oak shares some determinants with the Pseudomonas-Arabidopsis system. Photosynthesis-related transcripts were depleted in response to powdery mildew infection, but AcH 505 alleviated this inhibition, which suggested there is a fitness benefit for primed plants upon pathogen challenge. This study offers novel insights into the mechanisms of priming by actinobacteria and highlights their capacity to activate plant defense responses in the absence of pathogen challenge.
Prediction of the age at onset in spinocerebellar ataxia type 1, 2, 3 and 6
2014-04-29

Background The most common spinocerebellar ataxias (SCA)—SCA1, SCA2, SCA3, and SCA6—are caused by (CAG)n repeat expansion. While the number of repeats of the coding (CAG)n expansions is correlated with the age at onset, there are no appropriate models that include both affected and preclinical carriers allowing for the prediction of age at onset. Methods We combined data from two major European cohorts of SCA1, SCA2, SCA3, and SCA6 mutation carriers: 1187 affected individuals from the EUROSCA registry and 123 preclinical individuals from the RISCA cohort. For each SCA genotype, a regression model was fitted using a log-normal distribution for age at onset with the repeat length of the alleles as covariates. From these models, we calculated expected age at onset from birth and conditionally that this age is greater than the current age. Results For SCA2 and SCA3 genotypes, the expanded allele was a significant predictor of age at onset (−0.105±0.005 and −0.056±0.003) while for SCA1 and SCA6 genotypes both the size of the expanded and normal alleles were significant (expanded: −0.049±0.002 and −0.090±0.009, respectively; normal: +0.013±0.005 and −0.029±0.010, respectively). According to the model, we indicated the median values (90% critical region) and the expectancy (SD) of the predicted age at onset for each SCA genotype according to the CAG repeat size and current age. Conclusions These estimations can be valuable in clinical and research. However, results need to be confirmed in other independent cohorts and in future longitudinal studies. ClinicalTrials.gov, number NCT01037777 and NCT00136630 for the French patients.
Lipid droplet and early autophagosomal membrane targeting of Atg2A and Atg14L in human tumor cells
2014-04-29

Autophagy is a lysosomal bulk degradation pathway for cytoplasmic cargo, such as long-lived proteins, lipids, and organelles. Induced upon nutrient starvation, autophagic degradation is accomplished by the concerted actions of autophagy-related (ATG) proteins. Here we demonstrate that two ATGs, human Atg2A and Atg14L, colocalize at cytoplasmic lipid droplets (LDs) and are functionally involved in controlling the number and size of LDs in human tumor cell lines. We show that Atg2A is targeted to cytoplasmic ADRP-positive LDs that migrate bidirectionally along microtubules. The LD localization of Atg2A was found to be independent of the autophagic status. Further, Atg2A colocalized with Atg14L under nutrient-rich conditions when autophagy was not induced. Upon nutrient starvation and dependent on phosphatidylinositol 3-phosphate [PtdIns(3)P] generation, both Atg2A and Atg14L were also specifically targeted to endoplasmic reticulum-associated early autophagosomal membranes, marked by the PtdIns(3)P effectors double-FYVE containing protein 1 (DFCP1) and WD-repeat protein interacting with phosphoinositides 1 (WIPI-1), both of which function at the onset of autophagy. These data provide evidence for additional roles of Atg2A and Atg14L in the formation of early autophagosomal membranes and also in lipid metabolism.