julilili42/papers huggingface dataset:
The Pseudomonas type III effector HopQ1 activates cytokinin signaling and interferes with plant innate immunity
2013-10-11

Summary We characterized the molecular function of the P seudomonas syringae pv. tomato DC 3000 ( Pto ) effector HopQ1. In silico studies suggest that HopQ1 might possess nucleoside hydrolase activity based on the presence of a characteristic aspartate motif. Transgenic A rabidopsis lines expressing HopQ1 or HopQ1 aspartate mutant variants were characterized with respect to flagellin triggered immunity, phenotype and changes in phytohormone content by high‐performance liquid chromatography‐MS ( HPLC ‐ MS ). We found that HopQ1, but not its aspartate mutants, suppressed all tested immunity marker assays. Suppression of immunity was the result of a lack of the flagellin receptor FLS 2, whose gene expression was abolished by HopQ1 in a promoter‐dependent manner. Furthermore, HopQ1 induced cytokinin signaling in A rabidopsis and the elevation in cytokinin signaling appears to be responsible for the attenuation of FLS2 expression. We conclude that HopQ1 can activate cytokinin signaling and that moderate activation of cytokinin signaling leads to suppression of FLS2 accumulation and thus defense signaling.
Ammonium tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803 and the role of the psbA multigene family
2013-10-11

Abstract Ammonium is one of the major nutrients for plants, and a ubiquitous intermediate in plant metabolism, but it is also known to be toxic to many organisms, in particular to plants and oxygenic photosynthetic microorganisms. Although previous studies revealed a link between ammonium toxicity and photodamage in cyanobacteria under in vivo conditions, ammonium‐induced photodamage of photosystem II ( PSII ) has not yet been investigated with isolated thylakoid membranes. We show here that ammonium directly accelerated photodamage of PSII in S ynechocystis sp. strain PCC 6803, rather than affecting the repair of photodamaged PSII . Using isolated thylakoid membranes, it could be demonstrated that ammonium‐induced photodamage of PSII primarily occurred at the oxygen evolution complex, which has a known binding site for ammonium. Wild‐type S ynechocystis PCC 6803 cells can tolerate relatively high concentrations of ammonium because of efficient PSII repair. Ammonium tolerance requires all three psbA genes since mutants of any of the three single psbA genes are more sensitive to ammonium than wild‐type cells. Even the poorly expressed psbA1 gene, whose expression was studied in some detail, plays a detectable role in ammonium tolerance.
Screening for Protein-DNA Interactions by Automatable DNA-Protein Interaction ELISA
2013-10-11

DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA. Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed. Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation. To close this gap, we report an automatable DNA-protein-interaction (DPI)-ELISA screen of an optimized double-stranded DNA (dsDNA) probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs. In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation. Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus. We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP. As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences. In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi. Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1. A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding. This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts. Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a deeper understanding of gene regulation in any organism of choice.
Prognostic relevance of global histone 3 lysine 9 acetylation in ependymal tumors
2013-10-11

Object Ependymal tumors are highly variable in clinical and molecular behavior and affect both children and adults. Regarding the paucity of appropriate experimental models, the underlying molecular mechanisms of their behavioral variability are poorly understood. Considering the increasing evidence of epigenetic changes in various tumors, in addition to the preclinical success of epigenetic-based therapeutics in tumors of the CNS, epigenetic study of ependymal tumors is warranted. Methods Using immunohistochemistry, the authors investigated the patterns of global acetylation of lysine position 9 of histone 3 (H3K9Ac), an epigenetic marker of active gene transcription, in 85 ependymal tumors with various WHO grades and clinicopathological characteristics. Results Most of the nuclei in all ependymal tumors were H3K9Ac negative (mean ± SD 65.9% ± 26.5 vs 34.1% ± 26.5% positive, p &lt; 0.0001). Subependymomas had more H3K9Ac-positive nuclei (67.2% ± 10.2%) than myxopapillary ependymomas, ependymomas, and anaplastic ependymomas (p &lt; 0.05). Additionally, intracranial parenchymal tumors had significantly fewer H3K9Ac-positive nuclei (13.1% ± 21.9%) than tumors of other CNS localizations (p &lt; 0.001), and supratentorial ventricular tumors had the highest number of H3K9Ac-positive nuclei (66.4% ± 11.8%) among CNS ependymal tumors (p &lt; 0.0001). The H3K9Ac pattern in ependymal tumors also revealed prognostic significance such that tumors with less than 20% acetylated nuclei had a higher probability of recurrence than tumors with 20% or more acetylated nuclei (p = 0.0327), and recurrent tumors had significantly fewer H3K9Ac-positive nuclei than primary ones (16% ± 22.5% vs. 38% ± 25.8%; p &lt; 0.0001). However, the effect of tumor location on survival of patients was nonsignificant in a multivariate survival analysis, and H3K9 acetylation levels of tumors contributed independently to the survival of patients. In addition, ependymal tumors with more than or equal to 20% H3K9 acetylated cells had lower MIB-1 expression than those with less than 20% H3K9 acetylated cells (p &lt; 0.01). Conclusions Global H3K9Ac contributes independently to the prognosis of patients with ependymal tumors such that tumors with lower H3K9Ac values have a higher probability of recurrence and are more proliferative. Additionally, subependymomas have a higher H3K9Ac profile than other ependymal tumor subclasses, underlining their benign clinical behavior.
Ceremonial objects or household items? Non-destructive μ-XRD2and μ-XRF studies on three Neolithic hematite axes from Qatar
2013-10-11

Three small stone axes were collected by the joint Qatari-German South Qatar Survey Project (SQSP) at two places close to the eastern and western coast of Qatar in autumn 2012. Associated with settlement remains, flint artefacts and pieces of ʿUbaid pottery, the implements have been dated to the fifth millennium BCE. Non-destructive μ-XRD2 and μ-XRF analyses could, for the first time, prove the use of hematite as the raw material for the manufacture of these tools in Arabia. The absence of major hematite sources in the region and the special characteristics of hematite — a unique metallic shine of polished pieces and the blood-red colour that appears during the manufacturing process — suggest the highly symbolic character of these objects.
Freedom in the 1990s
2013-10-11

Abstract In the second half of the twentieth century there was a renaissance of liberalism and a new interest in freedom in modern Western industrialised nations. Theologians responded to the intellectual discourse in various ways while treating the concept of freedom in theology. Here three different engagements with the understanding of freedom and liberalism at the end of the century are introduced. The first is a critique of liberalism and rejection of modern accounts of freedom as autonomy. This account draws upon historical and theological resources in the presentation of modern liberalism as a negative development in theology and in understandings of society. In the article here, this first approach is presented in the context of its social and political orientation and contemporary context in the later twentieth century. While some of the contours of this first approach are viewed critically, one aspect of its intentions is praised. The second example is an adoption of the discourse of modern liberalism and a justification of it with an account of the Reformation as its progenitor. This account draws upon a narrative of progressive liberation in modern human history. The second approach is addressed here in its particular context after the Second World War and in the specific cultural and theological framework of the latter part of the twentieth century. While the revival of modern liberal theology in the latter part of the twentieth century is presented here as a necessary development in the wake of radical early twentieth century anti-liberalism, some of the sweeping claims of this approach are viewed critically. Finally, a third mediatory approach is presented. This general group sought to advance a form of the liberal theological tradition while also theologically challenging Enlightenment conceptions of autonomy. Three brief examples are drawn upon to illustrate this approach. One is concerned with providing orientation for the basic doctrinal question of human freedom and sin. The second example deals with the systematic theological specification of human freedom in the postmodern context and its relation to an understanding of divine freedom. The third example deals with the ethical implications of a theologically grounded understanding of freedom.
Bimodal immune activation in psoriasis
2013-10-12

Psoriasis is an immune-regulated skin disease with various clinical subtypes and disease activities. The majority of patients present with predominantly stable plaques. At the onset of new lesions, plaque-type psoriasis frequently demonstrates pin-sized and highly inflammatory papules sometimes with an inflammatory border. The histopathology of initial psoriasis differs from stable plaque-type psoriasis. Early lesions demonstrate innate immune cells with neutrophils, degranulating mast cells and macrophages. These are followed by interleukin (IL)-1-dependent T helper (Th)17 cells, finally resulting in the Th1-dominated immunopathology of stable plaque-type psoriasis, where mononuclear cells predominate with interspersed neutrophilic (Munro) microabscesses. These features suggest a bimodal immune pathway where alternate activation of either innate (autoinflammatory) or adaptive (autoimmune) immunity predominates. Neutrophilic infiltrations appear during early psoriasis with Munro abscesses. They are time limited and occur periodically, clinically best seen in linear nail pitting. These features strongly suggest a critical role for an IL-1-Th17-dominated autoinflammation in the initiation of psoriasis, followed by a Th1-dominated late-phase reaction. The concept of bimodal immune activation helps to explain results from therapeutic interventions that are variable and previously only partly understood.
Peri-Gondwanan terranes in the Romanian Carpathians: A review of their spatial distribution, origin, provenance, and evolution
2013-10-12

The basement of the Romanian Carpathians is made of Neoproterozoic to early Paleozoic peri-Gondwanan terranes variably involved in the Variscan orogeny, similarly to other basement terrains of Europe. They were hardly dismembered during the Alpine orogeny and traditionally have their own names in the three Carpathian areas. The Danubian domain of the South Carpathians comprises the Drăgşan and Lainici-Păiuş peri-Amazonian terranes. The Drăgşan terrane originated within the ocean surrounding Rodinia and docked with Rodinia at ∼800 Ma. It does not contain Cadomian magmatism and consequently it is classified as an Avalonian extra-Cadomian terrane. The Lainici-Păiuş terrane is a Ganderian fragment strongly modified by Cadomian subduction-related magmatism. It is attached to the Moesia platform. The Tisoviţa terrane is an ophiolite that marks the boundary between Drăgşan and Lainici-Păiuş terranes.\\nThe other basement terranes of the Romanian Carpathians originated close to the Ordovician North-African orogen, as a result of the eastern Rheic Ocean opening and closure. Except for the Sebeş-Lotru terrane that includes a lower metamorphic unit of Cadomian age, all the other terranes (Bretila, Tulgheş, Negrişoara and Rebra in the East Carpathians, Someş, Biharia and Baia de Arieş in the Apuseni mountains, Fagaraş, Leaota, Caraş and Padeş in the South Carpathians) represent late Cambrian–Ordovician rock assemblages. Their provenance, is probably within paleo-northeast Africa, close to the Arabian-Nubian shield.\\nThe late Cambrian–Ordovician terranes are defined here as Carpathian-type terranes. According to their lithostratigraphy and origin, some are of continental margin magmatic arc setting, whereas others formed in rift and back-arc environment and closed to passive continental margin settings. In a paleogeographic reconstruction, the continental margin magmatic arc terranes were first that drifted out, followed by the passive continental margin terranes with the back-arc terranes in their front. They accreted to Laurussia during the Variscan orogeny. Some of them (Sebeş-Lotru in South Carpathians and Baia de Arieş in Apuseni mountains) underwent eclogite-grade metamorphism. The Danubian terranes, the Bretila terrane and the Someş terrane were intruded by Variscan granitoids.
PEX5, the Shuttling Import Receptor for Peroxisomal Matrix Proteins, Is a Redox‐Sensitive Protein
2013-10-12

Peroxisome maintenance depends on the import of nuclear‐encoded proteins from the cytosol. The vast majority of these proteins is destined for the peroxisomal lumen and contains a C‐terminal peroxisomal targeting signal, called PTS1 . This targeting signal is recognized in the cytosol by the receptor PEX5 . After docking at the peroxisomal membrane and release of the cargo into the organelle matrix, PEX5 is recycled to the cytosol through a process requiring monoubiquitination of an N‐terminal, cytosolically exposed cysteine residue (Cys11 in the human protein). At present, the reason why a cysteine, and not a lysine residue, is the target of ubiquitination remains unclear. Here, we provide evidence that PTS1 protein import into human fibroblasts is a redox‐sensitive process. We also demonstrate that Cys11 in human PEX5 functions as a redox switch that regulates PEX5 activity in response to intracellular oxidative stress. Finally, we show that exposure of human PEX5 to oxidized glutathione results in a ubiquitination‐deficient PEX5 molecule, and that substitution of Cys11 by a lysine can counteract this effect. In summary, these findings reveal that the activity of PEX5 , and hence PTS1 import, is controlled by the redox state of the cytosol. The potential physiological implications of these findings are discussed.
A behavioral comparison of the common laboratory rat strains Lister Hooded, Lewis, Fischer 344 and Wistar in an automated homecage system
2013-10-12

Abstract Behavioral characterization is an important part of establishing novel animal models, but classical behavioral tests struggle to reveal conclusive results due to problems with both reproducibility and validity. On the contrary, automated homecage observations are believed to produce robust outcomes that relate more to natural animal behavior. However, information on the behavior of background strains from such observations, which could provide important reference material, is rare. For this reason, we compared the behavior of the commonly used Lister Hooded, Lewis, Fischer 344 and Wistar rats during 70 h of exposure to an automated homecage system at 2, 4 and 6 months of age. We found considerable strain differences in metabolic parameters, novelty‐induced and baseline activity‐related behavior as well as differences in the development of these parameters with age. The results are discussed in terms of advantages and disadvantages of the system compared to classical behavioral tests, as well as the system's ability to recreate common findings in literature .
Increased Mitotic and Proliferative Activity Are Associated With Worse Prognosis in Papillary Tumors of the Pineal Region
2013-10-12

Papillary tumors of the pineal region are rare glial tumors located in the vicinity of the third ventricle, the clinical behavior of which is often aggressive. Little is known about the prognostic markers that might aid to identify patients at increased risk for recurrence. Therefore, the prognostic value of histopathologic and clinical features was examined in a series of 21 patients. Median age of the 12 male and 9 female patients was 35 years (range, 10 to 56 y). On histopathologic examination, all tumors were characterized by loose papillary structures and tumor cells forming broad perivascular pseudorosettes showing cytokeratin expression. In addition, tumors showed increased cellularity (n=4; 19%), nuclear pleomorphism (n=4; 19%), solid growth (n=11; 52%), necrosis (n=8; 38%), increased mitotic activity (≥3 mitoses per 10 high-power fields [n=10; 48%]), and increased proliferation (Ki67/MIB1 index ≥10% [n=8/20; 40%]). Gross total resection could be achieved in 13/21 patients (62%). Postoperatively, 13 patients received radiotherapy and 4 patients chemotherapy. Median recurrence-free survival was 66 months in 19 patients, for whom detailed follow-up information was available. Twelve patients (63%) experienced tumor progression. Three patients (16%) died of disease. Among the clinical and histopathologic features examined, only increased mitotic activity (52 [8 to 96] vs. 68 [66 to 70] mo [median [95% confidence interval]]) and proliferative activity (29 [0 to 64] vs. 67 [44 to 90] mo) were significantly associated with recurrence (P<0.05). Tumors of the 3 patients who had succumbed to disease showed increased mitotic and proliferative activity. In conclusion, increased mitotic and proliferative activities are associated with worse prognosis in papillary tumors of the pineal region.
De novo partial deletion in GRID2 presenting with complicated spastic paraplegia
2013-10-12

ABSTRACT Introduction : Complex forms of spastic paraplegia (SPG) are rare and genetically heterogeneous. In apparently sporadic cases, analysis of known SPG genes often fails to reveal a mutation. Methods : We report a 24‐year‐old patient with a syndrome of spastic paraplegia, ataxia, frontotemporal dementia, and lower motor neuron involvement. Results : Screening of the patient's genome for copy number variation identified a novel 276 kb deletion spanning the first exon of the GRID2 gene. MRI scan showed atrophy of the cerebellum, and electromyography revealed a chronic disorder of motor neurons or their axons. A deletion in GRID2 , coding for the glutamate receptor delta‐2 subunit precursor protein, was excluded in either parent, suggesting that the deletion in the index patient occurred de novo . Conclusions : We hypothesize that the deletion identified here is the cause of our patient's clinical presentation, due to the resemblance to the GRID2 mutation phenotype in mouse models. Muscle Nerve 49 : 289–292, 2014
Processing order in dual-tasks when the duration of motor responses varies
2013-10-12

Recent studies reported that central processing duration influences processing order of two tasks in the psychological refractory period (PRP) paradigm. This study examined whether the duration of response execution influences the processing of task order. For this purpose, a tone discrimination task was combined with a letter discrimination task. Both tasks were presented in random order using different stimulus onset asynchronies (SOAs). In one condition, participants responded to each stimulus with a single key press (easy response condition). In the other condition, the tone task required a single key press, whereas the letter task required a more time-consuming key press-sequence (hard response condition). The results showed that participants tend to perform the tone task first more often when the response requirement for the letter task is hard, rather than easy. This result is consistent with the notion that participants optimize response scheduling in dual-task situations.
Optimizing tree and character compatibility across several phylogenetic trees
2013-10-12

Given a set R of rooted phylogenetic trees on overlapping taxa, it takes polynomial time to decide whether or not there exists a rooted phylogenetic tree that is compatible with R. Since not all evolutionary histories for a set of species can be explained by a single tree, it is natural to ask for the minimum number of rooted phylogenetic trees needed such that each tree in R is compatible with at least one tree. This paper shows that it is computationally hard to compute this minimum number. In particular, if R contains rooted triples (rooted binary phylogenetic trees on three leaves), it is NP-complete to decide whether there exist two rooted phylogenetic trees such that each rooted triple in R is compatible with at least one of the two trees. Furthermore, for a set Σ of binary characters and a positive integer k , we show that to decide if there exists a set P of k rooted phylogenetic trees such that each character in Σ is compatible with at least one tree in P is NP-complete for all k⩾3, but solvable in polynomial time for k=2. This generalizes the result for k=1, where it is well-known to be polynomial time.