julilili42/papers huggingface dataset:
Negative Selection In Vivo RNAi Screening Identifies a Ribosomal Protein As A New Therapeutic Target In Liver Cancer
2014-01-13

Due to the lack of treatment options hepatocellular carcinoma (HCC) represents the third most frequent cause of cancer related death. The major obstacle in HCC treatment is resistance to conventional chemotherapy and it becomes clear that new treatment strategies are urgently needed. We devised a system to conduct negative selection in vivo RNAi screens to identify new therapeutic target genes in Ras driven murine liver carcinomas. Multilocular invasive hepatocellular carcinomas develop after short latency when oncogenic Nras(G12V) is stably delivered into p19-/- mouse livers via transposable elements. As a proof of principle that RNAi mediated knockdown of target genes can cause lethality of Nras(G12V) driven liver tumors, we showed that stable expression of an shRNA targeting a cell essential DNA replication factor (replication protein 3, Rpa3) completely blocks Nras(G12V) driven tumorigenesis and that shRNA against Ras downstream target B-Raf reduced the tumor burden of injected mice. To identify vulnerabilities in Nras(G12V);p19-/- tumors that may be exploited as new therapeutic targets; we next performed a negative selection in vivo RNAi screen. Transposable elements co-expressing Nras(G12V) and a focused shRNA library were stably delivered into p19-/- mouse livers. The frequency of each shRNA in the library before delivery into hepatocytes and after liver tumor development (in tumor nodules) was quantified via deep sequencing and a comparison of obtained profiles identified hairpins against a ribosomal protein as top depleted. Functional validation experiments with different hairpins show that knockdown of our candidate gene strongly suppresses Nras(G12V) driven tumorigenesis in p19-/- mice whereas the observed tumor suppressive effects correlated with the knockdown efficiency. Suppression of the identified ribosomal candidate gene via RNAi causes a ribosomal stress response that drives murine p19-/- hepatoma cells into an irreversible cell cycle arrest. Interestingly, we show that the cells undergo a full senescence arrest and upregulate cytokines involved in activation of immune cells that mediate their clearance in vivo.
Multiplex in vivo RNAi screening instructs combination therapies to increase the therapeutic efficacy of the multikinase inhibitor sorafenib
2014-01-13

Hepatocellular carcinoma represents the third common cause of cancer death and the incidence is steadily increasing. Standard treatments are limited due to frequent tumor recurrence and a poor responsiveness to conventional chemotherapy. The approval of sorafenib, a small multikinase inhibitor as the first active systemic treatment against HCC, increases survival of HCC patients by less than 3 months. Thus, there is a strong need to understand the molecular mechanisms of sorafenib sensitivity and resistance in order to instruct sorafenib basedcombination therapies with higher therapeutic efficacy.
The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism
2014-01-14

Abstract The posttranslational regulation of proteins by lysine (Lys) acetylation has recently emerged to occur not only on histones, but also on organellar proteins in plants and animals. In particular, the catalytic activities of metabolic enzymes have been shown to be regulated by Lys acetylation. The Arabidopsis (Arabidopsis thaliana) genome encodes two predicted sirtuin-type Lys deacetylases, of which only Silent Information Regulator2 homolog (SRT2) contains a predicted presequence for mitochondrial targeting. Here, we have investigated the function of SRT2 in Arabidopsis. We demonstrate that SRT2 functions as a Lys deacetylase in vitro and in vivo. We show that SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport. Several of these protein complexes, such as the ATP synthase and the ATP/ADP carriers, show an increase in Lys acetylation in srt2 loss-of-function mutants. The srt2 plants display no growth phenotype but rather a metabolic phenotype with altered levels in sugars, amino acids, and ADP contents. Furthermore, coupling of respiration to ATP synthesis is decreased in these lines, while the ADP uptake into mitochondria is significantly increased. Our results indicate that SRT2 is important in fine-tuning mitochondrial energy metabolism.
High mutation detection rates in cerebral cavernous malformation upon stringent inclusion criteria: one‐third of probands are minors
2014-01-14

Abstract Cerebral cavernous malformations ( CCM ) are prevalent vascular malformations occurring in familial autosomal dominantly inherited or isolated forms. Once CCM are diagnosed by magnetic resonance imaging, the indication for genetic testing requires either a positive family history of cavernous lesions or clinical symptoms such as chronic headaches, epilepsy, neurological deficits, and hemorrhagic stroke or the occurrence of multiple lesions in an isolated case. Following these inclusion criteria, the mutation detection rates in a consecutive series of 105 probands were 87% for familial and 57% for isolated cases. Thirty‐one novel mutations were identified with a slight shift towards proportionally more CCM3 mutations carriers than previously published ( CCM1 : 60%, CCM2 : 18%, CCM3 : 22%). In‐frame deletions and exonic missense variants requiring functional analyses to establish their pathogenicity were rare: An in‐frame deletion within the C‐terminal FERM domain of CCM1 resulted in decreased protein expression and impaired binding to the transmembrane protein heart of glass ( HEG1 ). Notably, 20% of index cases carrying a CCM mutation were below age 10 and 33% below age 18 when referred for genetic testing. Since fulminant disease courses during the first years of life were observed in CCM1 and CCM3 mutation carriers, predictive testing of minor siblings became an issue.
Regulation of transport across cell membranes by the serum- and glucocorticoid-inducible kinase SGK1
2014-01-14

The serum- and glucocorticoid-inducible kinase 1 (SGK1) is genomically upregulated by cell stress including energy depletion and hyperosmotic shock as well as a variety of hormones including glucocorticoids, mineralocorticoids and TGFβ. SGK1 is activated by insulin, growth factors and oxidative stress via phosphatidylinositide-3-kinase, 3-phosphoinositide-dependent kinase PDK1 and mTOR. SGK1 is a powerful stimulator of Na(+)/K(+)-ATPase, carriers (e.g., NCC, NKCC, NHE1, NHE3, SGLT1, several amino acid transporters) and ion channels (e.g., ENaC, SCN5A, TRPV4-6, ORAI1/STIM1, ROMK, KCNE1/KCNQ1, GluR6, CFTR). Mechanisms employed by SGK1 in transport regulation include direct phosphorylation of target transport proteins, phosphorylation and thus activation of other transport regulating kinases, stabilization of membrane proteins by phosphorylation and thus inactivation of the ubiquitin ligase NEDD4-2, as well as stimulation of transport protein expression by upregulation transcription factors (e.g., nuclear factor kappa-B [NFκB]) and by fostering of protein translation. SGK1 sensitivity of pump, carrier and channel activities participate in the regulation of epithelial transport, cardiac and neuronal excitability, degranulation, platelet function, migration, cell proliferation and apoptosis. SGK1-sensitive functions do not require the presence of SGK1 but are markedly upregulated by SGK1. Accordingly, the phenotype of SGK1 knockout mice is mild. The mice are, however, less sensitive to excessive activation of transport by glucocorticoids, mineralocorticoids, insulin and inflammation. Moreover, excessive SGK1 activity contributes to the pathophysiology of hypertension, obesity, diabetes, thrombosis, stroke, inflammation, autoimmune disease, fibrosis and tumor growth.
Intranasal Angiotensin II in Humans Reduces Blood Pressure When Angiotensin II Type 1 Receptors Are Blocked
2014-01-14

Intranasal administration of angiotensin II (ANGII) affects blood pressure in a mode different from intravenously administered ANGII via a direct access to the brain bypassing the blood–brain barrier. This clinical study investigated blood pressure regulation after intranasal ANGII administration in healthy humans, whereas systemic, blood-mediated effects of ANGII were specifically blocked. In a balanced crossover design, men (n=8) and women (n=8) were intranasally administered ANGII (400 μg) or placebo after ANGII type 1 receptors had been blocked by pretreatment with valsartan (80 mg; 12 and 6 hours before intranasal administration). Plasma levels of ANGII, aldosterone, renin, vasopressin, and norepinephrine were measured; blood pressure and heart rate were recorded continuously. Intranasal ANGII acutely decreased blood pressure without altering the heart rate. Plasma levels of vasopressin and norepinephrine remained unaffected. Plasma ANGII levels were increased throughout the recording period. Aldosterone levels increased despite the peripheral ANGII type 1 receptor blockade, indicating an aldosterone escape phenomenon. In conclusion, intranasal ANGII reduces blood pressure in the presence of selective ANGII type 1 receptor blockade. Intranasal ANGII administration represents a useful approach for unraveling the role of this peptide in blood pressure regulation in humans.
Postchemotherapy Laparoscopic Retroperitoneal Lymph Node Dissection for Nonseminomatous Germ Cell Tumors Infiltrating the Great Vessels
2014-01-14

Laparoscopic RPLND may be considered a safe alternative concept for the management of post-chemotherapy NSGCT residuals involving the great vessels. Bilateral L-RPLND in patients with vascular infiltration is feasible and reproducible when laparoscopic vascular surgery can be reliably handled. All standard principles of open surgery are respected, and initial oncologic results are promising.
Stepwise withdrawal of inhaled corticosteroids in COPD patients receiving dual bronchodilation: WISDOM study design and rationale
2014-01-15

Long-acting bronchodilators in combination with inhaled corticosteroids (ICS) are recommended to decrease the risk of recurrent exacerbations in patients with Global initiative for chronic Obstructive Lung Disease (GOLD) stage 3-4 chronic obstructive pulmonary disease (COPD). There is increasing concern about the clinical benefit and long-term safety of ICS use in COPD patients. The WISDOM (Withdrawal of Inhaled Steroids During Optimised bronchodilator Management) study (NCT00975195) aims to evaluate the need for ICS use via stepwise withdrawal of ICS in COPD patients (GOLD 3-4 with a history of at least one exacerbation during the 12-month period prior to screening) receiving dual bronchodilation. During the 6-week run-in period, 2456 patients receive tiotropium 18 μg once daily, salmeterol 50 μg twice daily and fluticasone 500 μg twice daily. In a randomized, double-blind, parallel-group, active-controlled fashion, one group of patients continues to receive tiotropium, salmeterol and fluticasone, while the second group initiates stepwise withdrawal of fluticasone. The primary end point is time to first moderate or severe exacerbation following randomized treatment over 52 weeks. Lung function, symptoms and safety are also assessed. A sub-study aims to identify sub-populations and markers of steroid need. This study will determine the benefit of continued ICS therapy in combination with dual long-acting bronchodilators in COPD.
Once again, Erich Przywara and the Jews: A response to John Betz with a brief look into the Nazi correspondences on Przywara and Stimmen der Zeit
2014-01-15

Abstract In this article, I respond to John Betz (University of Notre Dame, USA) who has recently rejected claims that I have made about Erich Przywara’s anti- Semitism and his relationship to Nazi era ideology. Although I admire much of Przywara’s theology and have great sympathy for the teaching about the analogy of being, in this article I address some of the problems of Przywara’s work. I address literature from Przywara on the Jews where he talks about the essence of “the Jew” as “restless” and “revolutionary,” and where he brings up the “wandering Jew” theme or claims Judaism is an “insolent disturber” of the (German) “folkdom.” Przywara’s rejection of “Jewish messianism” and his claims about the “basic tension of the Jew” are also addressed. I analyze his conception of the essence of “the Jew” as, among other things, a “rising will of destruction” and his claim that “Christianity” ultimately becomes the “enemy” of Judaism. Beyond these things, Przywara’s desire to “overcome” Judaism with the right “weapons” is addressed. I also draw attention to his rejection of “Jewish capitalism” and his justification of “the hatred towards the Jews in world history.” In addition to this, his use of ideologically charged Nazi terminology, such as “host-peoples,” and his support of Catholic integralism in Nazi Germany are addressed. Furthermore, Przywara’s remarks (to a leading Nazi representative and ideologue, Hanns Johst) on “the positive sense” of the German “movements” (i. e. National Socialism) in the 1930s are presented. I also show that Przywara”s work was praised by a leading representative and ideologue of National Socialism (Otto Dietrich). With this, I address the internal Nazi correspondences on the very influential German Catholic Jesuit journal titled Stimmen der Zeit
Nutrient Limitation Governs Staphylococcus aureus Metabolism and Niche Adaptation in the Human Nose
2014-01-16

Colonization of the human nose by Staphylococcus aureus in one-third of the population represents a major risk factor for invasive infections. The basis for adaptation of S. aureus to this specific habitat and reasons for the human predisposition to become colonized have remained largely unknown. Human nasal secretions were analyzed by metabolomics and found to contain potential nutrients in rather low amounts. No significant differences were found between S. aureus carriers and non-carriers, indicating that carriage is not associated with individual differences in nutrient supply. A synthetic nasal medium (SNM3) was composed based on the metabolomics data that permits consistent growth of S. aureus isolates. Key genes were expressed in SNM3 in a similar way as in the human nose, indicating that SNM3 represents a suitable surrogate environment for in vitro simulation studies. While the majority of S. aureus strains grew well in SNM3, most of the tested coagulase-negative staphylococci (CoNS) had major problems to multiply in SNM3 supporting the notion that CoNS are less well adapted to the nose and colonize preferentially the human skin. Global gene expression analysis revealed that, during growth in SNM3, S. aureus depends heavily on de novo synthesis of methionine. Accordingly, the methionine-biosynthesis enzyme cysteine-γ-synthase (MetI) was indispensable for growth in SNM3, and the MetI inhibitor DL-propargylglycine inhibited S. aureus growth in SNM3 but not in the presence of methionine. Of note, metI was strongly up-regulated by S. aureus in human noses, and metI mutants were strongly abrogated in their capacity to colonize the noses of cotton rats. These findings indicate that the methionine biosynthetic pathway may include promising antimicrobial targets that have previously remained unrecognized. Hence, exploring the environmental conditions facultative pathogens are exposed to during colonization can be useful for understanding niche adaptation and identifying targets for new antimicrobial strategies.
Seasonal controls on grassland microbial biogeography: Are they governed by plants, abiotic properties or both?
2014-01-16

Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10&amp;nbsp;m&amp;nbsp;&amp;times;&amp;nbsp;10&amp;nbsp;m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns.
Biosynthetic Origin of the Antibiotic Cyclocarbamate Brabantamide A (SB‐253514) in Plant‐Associated Pseudomonas.
2014-01-16

Abstract Within the framework of our genome‐based program to discover new antibiotic lipopeptides from Pseudomonads, brabantamides A–C were isolated from plant‐associated Pseudomonas sp. SH‐C52. Brabantamides A–C displayed moderate to high in vitro activities against Gram‐positive bacterial pathogens. Their shared structure is unique in that they contain a 5,5‐bicyclic carbamate scaffold. Here, the biosynthesis of brabantamide A (SB‐253514) was studied by a combination of bioinformatics, feeding experiments with isotopically labelled precursors and in vivo and in vitro functional analysis of enzymes encoded in the biosynthetic pathway. The studies resulted in the deduction of all biosynthetic building blocks of brabantamide A and revealed an unusual feature of this metabolite: its biosynthesis occurs via an initially formed linear di‐lipopeptide that is subsequently rearranged by a novel FAD‐dependent Baeyer–Villiger monooxygenase.
In Vivo Tracking of Th1 Cells by PET Reveals Quantitative and Temporal Distribution and Specific Homing in Lymphatic Tissue
2014-01-16

Our protocol permits the detection of Th1 cells in single LNs and enables temporal in vivo monitoring of T-cell homing over 48 h. This work enables future applications for (64)Cu-PTSM-labeled T cells in clinical trials and novel therapy concepts focusing on T-cell-based immunotherapies of autoimmune diseases or cancer.
High‐resolution quantitative sodium imaging at 9.4 tesla
2014-01-16

Purpose Investigation of the feasibility to perform high‐resolution quantitative sodium imaging at 9.4 Tesla (T). Methods A proton patch antenna was combined with a sodium birdcage coil to provide a proton signal without compromising the efficiency of the X‐nucleus coil. Sodium density weighted images with a nominal resolution of 1 × 1 × 5 mm 3 were acquired within 30 min with an ultrashort echo time sequence. The methods used for signal calibration as well as for B 0 , B 1 , and off‐resonance correction were verified on a phantom and five healthy volunteers. Results An actual voxel volume of roughly 40 μL could be achieved at 9.4T, while maintaining an acceptable signal‐to‐noise ratio (8 for brain tissue and 35 for cerebrospinal fluid). The measured mean sodium concentrations for gray and white matter were 36 ± 2 and 31 ± 1 mmol/L of wet tissue, which are comparable to values previously reported in the literature. Conclusion The reduction of partial volume effects is essential for accurate measurement of the sodium concentration in the human brain. Ultrahigh field imaging is a viable tool to achieve this goal due to its increased sensitivity. Magn Reson Med 73:342–351, 2015. © 2014 Wiley Periodicals, Inc.
Machine Learning Estimates of Natural Product Conformational Energies
2014-01-16

Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP), mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures.
Mutations in the substrate binding site of human heat‐shock protein 70 indicate specific interaction with HLA‐DR outside the peptide binding groove
2014-01-16

Summary Heat‐shock protein 70 (Hsp70)–peptide complexes are involved in MHC class I ‐ and II ‐restricted antigen presentation, enabling enhanced activation of T cells. As shown previously, mammalian cytosolic Hsp70 (Hsc70) molecules interact specifically with HLA ‐ DR molecules. This interaction might be of significance as Hsp70 molecules could transfer bound antigenic peptides in a ternary complex into the binding groove of HLA ‐ DR molecules. The present study provides new insights into the distinct interaction of Hsp70 with HLA ‐ DR molecules. Using a quantitative binding assay, it could be demonstrated that a point mutation of amino acids alanine 406 and valine 438 in the substrate binding pocket led to reduced peptide binding compared with the wild‐type Hsp70 whereas HLA ‐ DR binding remains unaffected. The removal of the C‐terminal lid neither altered the substrate binding capacity nor the Hsp70 binding characteristics to HLA ‐ DR . A truncated variant lacking the nucleotide binding domain showed no binding interactions with HLA ‐ DR . Furthermore, the truncated ATP ase subunit of constitutively expressed Hsc70 revealed similar binding affinities to HLA ‐ DR compared with the complete Hsc70. Hence, it can be assumed that the Hsp70– HLA ‐ DR interaction takes place outside the peptide binding groove and is attributed to the ATP ase domain of HSP70 molecules. The Hsp70‐chaperoned peptides might thereby be directly transferred into the binding groove of HLA ‐ DR , so enabling enhanced presentation of the peptide on antigen‐presenting cells and leading to an improved proliferation of responding T cells as shown previously.