julilili42/papers huggingface dataset:
RNAi and CRISPR/Cas9 Based In Vivo Models for Drug Discovery
2017-12-07

With the advent of RNAi and more recently CRISPR/Cas9 technologies, we now have an advanced platform to rapidly generate disease and perform target validation and toxicity assessment of novel candidate targets all in the same animal. Having previously engineered a miRE scaffold for enhanced shRNA processing and now with the introduction of a powerful new SplashRNA algorithm for accurate shRNA prediction, we have brought RNAi technologies to its peak, by increasing potency and reducing off-target effects, such that it can be effectively exploited to preclinically mimic drug therapy and even combination therapy not only in vitro but also in live mice. Here, we take advantage of doxycycline-inducible RNAi mice to identify on-target toxicities associated inhibition of Rpl15 ,a novel gene target previously identified through screening as a potent therapeutic target for the treatment of HCC. We demonstrate that sustained Rpl15 suppression results in an impaired intestinal barrier with subsequent weight loss. Heterozygous mutation or deletion of Rpl15 has been associated with Diamond Blackfan Anemia in humans and we therefore analyzed our mice for hematological phenotypes. Peripheral blood counts revealed only a non-significant decrease in erythrocytes and hemoglobin in Rpl15 knockdown mice compared to mice expressing a control shRNA. However, we found that Rpl15 suppression resulted in a strong decrease in spleen size and histopathological analyses revealed signs of increased siderosis. Importantly, phenotypic toxicities are not observed following doxycycline removal and reexpression of Rpl15, thus suggesting that a therapeutic window of treatment exists for inhibition of this essential gene. By combining this approach with in situ delivery of Cas9/gRNAs, we proceed one step further to rapidly develop HCC and validate Rpl15 as potent target of HCC in vivo . These data showcase how synergizing our RNAi and CRISPR/Cas9 genetic toolbox will help facilitate drug discovery research and increase our confidence in predicting drug responses in humans into a new era. Disclosures Premsrirut: Mirimus Inc.: Employment, Equity Ownership, Membership on an entity9s Board of Directors or advisory committees. Wang: Mirimus Inc.: Employment. Yang: Mirimus Inc.: Employment. Fellmann: Mirimus Inc.: Consultancy, Equity Ownership. Dow: Mirimus Inc.: Consultancy. Zuber: Mirimus Inc.: Consultancy. Lowe: Mirimus Inc.: Consultancy.
Dysregulation of the ASPP Protein Family (Apoptosis Stimulating Proteins of TP53) Is a Common Feature in High-Risk Acute Myeloid Leukemia (AML)
2017-12-07

Abstract Inactivation of the TP53 pathway is a frequent event in human cancers promoting tumorigenesis and resistance to chemotherapy. Inactivating TP53 mutations are uncommon in non-complex karyotype leukemias suggesting that the TP53 pathway must be inactivated by other mechanisms. ASPP proteins are a family of TP53-binding proteins consisting of three members: pro-apoptotic ASPP1 and ASPP2 and apoptosis-inhibiting iASPP. ASPPs control induction of apoptosis via direct interactions with TP53 but also other key proteins such as BCL-2/BXL-xl. We here reveal universal dysregulation of ASPPs in AML correlating with chemotherapy failure and provide a novel therapeutic target. mRNA and protein expression levels of ASPP1, ASPP2 and iASPP were determined in freshly isolated native patient samples (n=120) as well as healthy bone marrow donors (n=34). To mimick direct implications of the specific ASPP protein in response to chemotherapy, ASPPs were stably silenced in leukemia cell lines (MOLM14, Jurkat, HL60, NB4 or OCI-3), native patient blasts and bone marrow donor samples using a retroviral shRNA approach. Sensitivity towards standard chemotherapeutics was assessed using XTT viability and annexin V-based apoptosis assays. Transfection with an empty vector served as a negative control. Interestingly, all family members, ASPP1 (p=0.001), ASPP2 (p=0.02) and iASPP (p=0.001) were found to be significantly altered in AML compared to healthy donors. Subgroup analyses revealed association with high-risk features and failure towards induction chemotherapy. Importantly, dysregulation was not exclusive and may affect several family members - which was associated with dismal outcome. Retroviral ASPP1/2 -interference lead to perturbed proliferation capacities (up to 3-fold increase) and attenuated apoptosis in response to chemotherapy in all tested models. Vice versa, inhibition of iASPP resulted in attenuated proliferation and an increase in apoptosis. For ASPP1/2, we demonstrate promoter methylation and restoration of protein expression upon treatment with aza-nucleosides. Additional BCL-2 inhibition (using venetoclax) consequently resulted in superadditive, proapoptotic efficacy compared to the knockdown cell strains. To summarize, dysfunctional regulation of ASPP proteins is a common feature in high-risk leukemias associated with treatment failure. Restoring pro-apoptotic ASPP1/2 function using hypomethylating agents and combination with proapoptotic agents such as venetoclax may overcome therapy resistance in these settings. Disclosures No relevant conflicts of interest to declare.
Cell-Stage Dependent Outcomes of the NAMPT/SIRT2-Mediated Activation of LMO2 By Deacetylation in Normal Hematopoiesis and in T-ALL
2017-12-07

Abstract NAMPT (nicotinamide phosphoribosyltransferase) regulates cellular functions through the protein deacetylation activity of NAD+-dependent sirtuins (SIRT). Here we demonstrated that NAMPT is indispensable for hematopoiesis and leukemogenesis through SIRT2-mediated deacetylation and activation of the hematopoietic transcription factor, LMO2 (LIM domain only 2). LMO2 is essential for the blood cell formation through the interaction with LIM Domain Binding 1 (LDB1) protein and activation of the TAL1 transcriptional complex. We found that NAMPT/SIRT2-mediated deacetylation of LMO2 on two evolutionary highly conserved lysines (K74 and K78) enables its interaction with LDB1 protein, activation of the TAL1 complex target genes (e.g. GATA1, KDR, KLF1) and hematopoietic differentiation. NAMPT- or SIRT2 inhibition abrogated LMO2 deacetylation and early hematopoietic differentiation of the induced pluripotent stem cells (iPSCs) in vitro as well as blood cell formation in zebrafish embryos in vivo on 24 hours post fertilization. Intriguingly, transfection of NAMPT- compromised zebrafish embryos with the deacetylation-mimic LMO2 mutant restore defective hematopoiesis, demonstrating the essential role of LMO2 deacetylation on K74 and K78 in NAMPT-mediated early hematopoiesis. Intriguingly, LMO2 is also known as an oncogene, which hyper-activation transforms lymphoid progenitor cells into T-cell acute lymphoblastic leukemia (T-ALL) blasts. We found, that NAMPT- or SIRT2 inhibition markedly suppressed proliferation of LMO2-expressing T-ALL cells in vitro and in zebrafish xenograft model in vivo . It was in line with impaired LMO2:LDB1 interaction and downregulation of T-ALL-specific LMO2 target genes such as HHEX. Taken together, we identified a new molecular mechanism of LMO2 activation by NAMPT/SIRT2-mediated deacetylation, which may explain the pathogenesis of hematopoietic diseases, involving disturbed TAL1 complex functions. Moreover, we found, that targeting of LMO2 deacetylation by NAMPT/SIRT2 inhibition may be a potential novel therapy for LMO2-related T-ALL. Disclosures No relevant conflicts of interest to declare.
Examination of the Shared Genetic Basis of Anorexia Nervosa and Obsessive-Compulsive Disorder
2017-12-08

ABSTRACT Anorexia nervosa (AN) and obsessive-compulsive disorder (OCD) are often comorbid and likely to share genetic risk factors. Hence, we examine their shared genetic background using a crossdisorder GWAS meta-analysis of 3,495 AN cases, 2,688 OCD cases and 18,013 controls. We confirmed a high genetic correlation between AN and OCD (r g = 0.49 ± 0.13, p = 9.07×10 −7 ) and a sizable SNP heritability (SNP h 2 = 0.21 ± 0.02) for the cross-disorder phenotype. Although no individual loci reached genome-wide significance, the cross-disorder phenotype showed strong positive genetic correlations with other psychiatric phenotypes (e.g., bipolar disorder, schizophrenia, neuroticism) and negative correlations with metabolic phenotypes (e.g., BMI, triglycerides). Follow-up analyses revealed that although AN and OCD overlap heavily in their shared risk with other psychiatric phenotypes, the relationship with metabolic and anthropometric traits is markedly stronger for AN than for OCD. We further tested whether shared genetic risk for AN/OCD was associated with particular tissue or cell-type gene expression patterns and found that the basal ganglia and medium spiny neurons were most enriched for AN/OCD risk, consistent with neurobiological findings for both disorders. Our results confirm and extend genetic epidemiological findings of shared risk between AN and OCD and suggest that larger GWASs are warranted.
Don’t believe in a paradigm that you haven’t manipulated yourself!
2017-12-08

Abstract A speaker may conceptualise a situation from three different modal ‘perspectives’: epistemic, evidential, and attitudinal. Languages differ in which of these concepts they perspectivise and how a grammaticalised concept may be extended to the other two. ‘Lesser-known’ languages tend to be misrepresented in the typological literature. E.g., the Modern Tibetic languages, including the Ladakhi dialects, are said to have grammaticalised the concept of evidentiality . However, their ‘evidential’ systems differ from the cross-linguistically acknowledged evidential systems, in that speaker attitude is co-grammaticalised and knowledge based on perception shares properties with knowledge based on inferences. DeLancey therefore claimed that these systems also encode mirativity . The starting point for the development of these typologically rather uncommon ‘evidential’ systems was a lexical marker for non-commitment (or admirativity ): the auxiliary ḥdug .
On the existence of a cherry-picking sequence
2017-12-08

Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences. Such a sequence is a particular ordering on the leaves of the trees in P. However, it is well-known that not all collections of phylogenetic trees have a cherry-picking sequence. In this paper, we show that the problem of deciding whether or not P has a cherry-picking sequence is NP-complete for when P contains at least eight rooted binary phylogenetic trees. Moreover, we use automata theory to show that the problem can be solved in polynomial time if the number of trees in P and the number of cherries in each such tree are bounded by a constant.
A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ε
2017-12-09

ABSTRACT Casein kinase 1 (CK1) plays central roles in various signal transduction pathways and performs many cellular activities. For many years CK1 was thought to act independently of modulatory subunits and in a constitutive manner. Recently, DEAD box RNA helicases, in particular DEAD box RNA helicase 3 X-linked (DDX3X), were found to stimulate CK1 activity in vitro. In order to observe CK1 activity in living cells and to study its interaction with DDX3X, we developed a CK1-specific FRET biosensor. This tool revealed that DDX3X is indeed required for full CK1 activity in living cells. Two counteracting mechanisms control the activity of these enzymes. Phosphorylation by CK1 impairs the ATPase activity of DDX3X and RNA destabilizes the DDX3X–CK1 complex. We identified possible sites of interaction between DDX3X and CK1. While mutations identified in the DDX3X genes of human medulloblastoma patients can enhance CK1 activity in living cells, the mechanism of CK1 activation by DDX3X points to a possible therapeutic approach in CK1-related diseases such as those caused by tumors driven by aberrant Wnt/β-catenin and Sonic hedgehog (SHH) activation. Indeed, CK1 peptides can reduce CK1 activity.
Heterocycles [h]-fused onto 4-oxoquinoline-3-carboxylic acid. Part XII: synthesis of 5-fluoro-7-oxodihydo[1,3,4]thiadiazino [5,6-h]quinoline-8-carboxylic acid and ester
2017-12-09

Abstract Direct interaction of dithizone with 7-chloro-6- fluoro-8-nitro-4-oxoquinoline-3-carboxylic acid or with its ester delivered the corresponding novel 1,3,4-thiadiazino [5,6- h ]quinoline 3-carboxylic acid, or its ester which was then hydrolyzed to the respective acid. Structures of the latter tricyclic hybrids were deduced from analytical and spectral data and confirmed by single crystal X-ray structure determination of the ester derivative. The free acid showed moderate activity against Staphylococcus aureus with a MIC value of 25 μg mL −1 .
Testing the Performance and Accuracy of the relxill Model for the Relativistic X-Ray Reflection from Accretion Disks
2017-12-10

Abstract The reflection spectroscopic model relxill is commonly implemented in studying relativistic X-ray reflection from accretion disks around black holes. We present a systematic study of the model’s capability to constrain the dimensionless spin and ionization parameters from ∼6000 Nuclear Spectroscopic Telescope Array ( NuSTAR ) simulations of a bright X-ray source employing the lamp-post geometry. We employ high-count spectra to show the limitations in the model without being confused with limitations in signal-to-noise. We find that both parameters are well-recovered at 90% confidence with improving constraints at higher reflection fraction, high spin, and low source height. We test spectra across a broad range—first at 10 6 –10 7 and then ∼10 5 total source counts across the effective 3–79 keV band of NuSTAR , and discover a strong dependence of the results on how fits are performed around the starting parameters, owing to the complexity of the model itself. A blind fit chosen over an approach that carries some estimates of the actual parameter values can lead to significantly worse recovery of model parameters. We further stress the importance to span the space of nonlinear-behaving parameters like carefully and thoroughly for the model to avoid misleading results. In light of selecting fitting procedures, we recall the necessity to pay attention to the choice of data binning and fit statistics used to test the goodness of fit by demonstrating the effect on the photon index Γ. We re-emphasize and implore the need to account for the detector resolution while binning X-ray data and using Poisson fit statistics instead while analyzing Poissonian data.
Platinum loaded tin dioxide: a model system for unravelling the interplay between heterogeneous catalysis and gas sensing
2017-12-11

The presented work unravels the complex structure–function-relationships of Pt-loaded SnO<sub>2</sub>, namely the sensitization by a Fermi-control mechanism and relation of catalytic activity and gas sensing effect.
Petroclival Meningiomas: Factors Determining the Choice of Approach
2017-12-11

Objectives To review a surgical series of petroclival meningiomas and the factors considered in the choice of approach. Design Retrospective review. Setting The study was conducted in a university hospital in southern Brazil. Participants Twenty-two patients with petroclival meningioma originating from the upper two-thirds of the clivus medial to the fifth cranial nerve. Main Outcome Measures Gross-total resection, mortality, major morbidity, new cranial nerve deficits and tumor progression or recurrence. Results Retrosigmoid approach was used in tumors &lt;3 cm and in those at or below the internal auditory meatus. Posterior petrosectomy was performed for tumors extending into the middle fossa. Gross-total resection was performed in 11 patients (50%). The mean follow-up time was 32 months (6–75 months). There were four cases of tumor progression or recurrence, which were treated with radiosurgery. Conclusions Resection of petroclival meningiomas remains challenging. In most cases, the retrosigmoid approach was sufficient, without affecting the degree of tumor resection. Petrosal approaches were reserved for patients with tumor extension into the middle fossa.
Attitudes Toward e-Health: The Otolaryngologists' Point of View
2017-12-11

The otolaryngologists are well prepared and have an overall positive attitude toward e-health for deeper use in cross-sectoral care. Therefore, e-health in otolaryngology needs more attention and resources for further studies, especially with a focus on quality and safety of care.
In Vivo Imaging of Glial Activation after Unilateral Labyrinthectomy in the Rat: A [18F]GE180-PET Study
2017-12-11

The functional relevance of reactive gliosis for recovery from acute unilateral vestibulopathy is unknown. In the present study, glial activation was visualized <i>in vivo</i> by [<sup>18</sup>F]GE180-PET in a rat model of unilateral labyrinthectomy (UL) and compared to behavioral vestibular compensation (VC) overtime. 14 Sprague-Dawley rats underwent a UL by transtympanic injection of bupivacaine/arsenilate, 14 rats a SHAM UL (injection of normal saline). Glial activation was depicted with [<sup>18</sup>F]GE180-PET and <i>ex vivo</i> autoradiography at baseline and 7, 15, 30 days after UL/SHAM UL. Postural asymmetry and nystagmus were registered at 1, 2, 3, 7, 15, 30 days after UL/SHAM UL. Signs of vestibular imbalance were found only after UL, which significantly decreased until days 15 and 30. In parallel, [<sup>18</sup>F]GE180-PET and <i>ex vivo</i> autoradiography depicted glial activation in the ipsilesional vestibular nerve and nucleus on days 7 and 15 after UL. Correlation analysis revealed a strong negative association of [<sup>18</sup>F]GE180 uptake in the ipsilesional vestibular nucleus on day 7 with the rate of postural recovery (<i>R</i> = -0.90, <i>p</i> < 0.001), suggesting that glial activation accelerates VC. In conclusion, glial activation takes place in the ipsilesional vestibular nerve and nucleus within the first 30 days after UL in the rat and can be visualized <i>in vivo</i> by [<sup>18</sup>F]GE180-PET.
An efficient synthesis of 1,6-anhydro-N-acetylmuramic acid from N-acetylglucosamine
2017-12-11

A novel synthesis of 1,6-anhydro- N -acetylmuramic acid is described, which proceeds in only five steps from the cheap starting material N -acetylglucosamine. This efficient synthesis should enable future studies into the importance of 1,6-anhydromuramic acid in bacterial cell wall recycling processes.
Can Empirical Research Predict the Future of the Church?
2017-12-11

Abstract This article first discusses the question of how empirical research can contribute to the ongoing discussions concerning the future of the church. Among others, German research on church membership is used as a case study for gaining insights into the interplay between theoretical assumptions, empirical research and designing strategies for church development. The need for comparisons over time, for longitudinal studies and the identification of long-term predictors is discussed. Against this background, recent research on confirmation work in Germany and Europe is taken up as an example. The article draws on data from a European study on confirmation work with a longitudinal research approach. The results show that confirmation work, as one of the major educational programs of the Protestant Church, can influence adolescents’ views of Christian faith and the church. Predictors for future commitment to the church in terms of believing, belonging and volunteerism are not only dependent on religious socialization in childhood but also on experiences and activities during confirmation time in adolescence.
Role of Perivascular Adipose Tissue in Health and Disease
2017-12-11

Perivascular adipose tissue (PVAT) is cushion of fat tissue surrounding blood vessels, which is phenotypically different from other adipose tissue depots. PVAT is composed of adipocytes and stromal vascular fraction, constituted by different populations of immune cells, endothelial cells, and adipose-derived stromal cells. It expresses and releases an important number of vasoactive factors with paracrine effects on vascular structure and function. In healthy individuals, these factors elicit a net anticontractile and anti-inflammatory paracrine effect aimed at meeting hemodynamic and metabolic demands of specific organs and regions of the body. Pathophysiological situations, such as obesity, diabetes or hypertension, induce changes in its amount and in the expression pattern of vasoactive factors leading to a PVAT dysfunction in which the beneficial paracrine influence of PVAT is shifted to a pro-oxidant, proinflammatory, contractile, and trophic environment leading to functional and structural cardiovascular alterations and cardiovascular disease. Many different PVATs surrounding a variety of blood vessels have been described and exhibit regional differences. Both protective and deleterious influence of PVAT differs regionally depending on the specific vascular bed contributing to variations in the susceptibility of arteries and veins to vascular disease. PVAT therefore, might represent a novel target for pharmacological intervention in cardiovascular disease. © 2018 American Physiological Society. Compr Physiol 8:23-59, 2018.
A 1-phytase type III effector interferes with plant hormone signaling
2017-12-12

Abstract Most Gram-negative phytopathogenic bacteria inject type III effector (T3E) proteins into plant cells to manipulate signaling pathways to the pathogen’s benefit. In resistant plants, specialized immune receptors recognize single T3Es or their biochemical activities, thus halting pathogen ingress. However, molecular function and mode of recognition for most T3Es remains elusive. Here, we show that the Xanthomonas T3E XopH possesses phytase activity, i.e., dephosphorylates phytate ( myo -inositol- hexakis phosphate, InsP 6 ), the major phosphate storage compound in plants, which is also involved in pathogen defense. A combination of biochemical approaches, including a new NMR-based method to discriminate inositol polyphosphate enantiomers, identifies XopH as a naturally occurring 1-phytase that dephosphorylates InsP 6 at C1. Infection of Nicotiana benthamiana and pepper by Xanthomonas results in a XopH-dependent conversion of InsP 6 to InsP 5. 1-phytase activity is required for XopH-mediated immunity of plants carrying the Bs7 resistance gene, and for induction of jasmonate- and ethylene-responsive genes in N. benthamiana .