Natural products play a significant role in drug discovery and development. Many topological pharmacophore patterns are common between natural products and commercial drugs. A better understanding of ...the specific physicochemical and structural features of natural products is important for corresponding drug development. Several encyclopedias of natural compounds have been composed, but the information remains scattered or not freely available. The first version of the Supernatural database containing ∼ 50,000 compounds was published in 2006 to face these challenges. Here we present a new, updated and expanded version of natural product database, Super Natural II (http://bioinformatics.charite.de/supernatural), comprising ∼ 326,000 molecules. It provides all corresponding 2D structures, the most important structural and physicochemical properties, the predicted toxicity class for ∼ 170,000 compounds and the vendor information for the vast majority of compounds. The new version allows a template-based search for similar compounds as well as a search for compound names, vendors, specific physical properties or any substructures. Super Natural II also provides information about the pathways associated with synthesis and degradation of the natural products, as well as their mechanism of action with respect to structurally similar drugs and their target proteins.
Purpose
Design, implementation, evaluation, and application of a 32‐channel Self‐Grounded Bow‐Tie (SGBT) transceiver array for cardiac MR (CMR) at 7.0T.
Methods
The array consists of 32 compact SGBT ...building blocks. Transmission field (B1+) shimming and radiofrequency safety assessment were performed with numerical simulations and benchmarked against phantom experiments. In vivo B1+ efficiency mapping was conducted with actual flip angle imaging. The array’s applicability for accelerated high spatial resolution 2D FLASH CINE imaging of the heart was examined in a volunteer study (n = 7).
Results
B1+ shimming provided a uniform field distribution suitable for female and male subjects. Phantom studies demonstrated an excellent agreement between simulated and measured B1+ efficiency maps (7% mean difference). The SGBT array afforded a spatial resolution of (0.8 × 0.8 × 2.5) mm3 for 2D CINE FLASH which is by a factor of 12 superior to standardized cardiovascular MR (CMR) protocols. The density of the SGBT array supports 1D acceleration of up to R = 4 (mean signal‐to‐noise ratio (whole heart) ≥ 16.7, mean contrast‐to‐noise ratio ≥ 13.5) without impairing image quality significantly.
Conclusion
The compact SGBT building block facilitates a modular high‐density array that supports accelerated and high spatial resolution CMR at 7.0T. The array provides a technological basis for future clinical assessment of parallel transmission techniques.
Autophagy is a ubiquitous catabolic process that causes cellular bulk degradation of cytoplasmic components and is generally associated with positive effects on health and longevity. Inactivation of ...autophagy has been linked with detrimental effects on cells and organisms. The antagonistic pleiotropy theory postulates that some fitness-promoting genes during youth are harmful during aging. On this basis, we examined genes mediating post-reproductive longevity using an RNAi screen. From this screen, we identified 30 novel regulators of post-reproductive longevity, including
Through downstream analysis of
, we identified that the inactivation of genes governing the early stages of autophagy up until the stage of vesicle nucleation, such as
, strongly extend both life span and health span. Furthermore, our data demonstrate that the improvements in health and longevity are mediated through the neurons, resulting in reduced neurodegeneration and sarcopenia. We propose that autophagy switches from advantageous to harmful in the context of an age-associated dysfunction.
Even if considered a cumulative and not a proliferative CD5+ B-cell neoplasm, chronic lymphocytic leukemia (CLL) has a proliferation rate higher than that recognized earlier, especially in the ...lymphoid tissues. Some patients with CLL develop a clinical syndrome entitled Richter syndrome (RS). Understanding CLL genetics and epigenetics may help to elucidate the molecular basics of the clinical heterogeneity of this type of malignancy. In the present project we aimed to identify a microRNA species that can predict the evolution of therapy-resistant CLL towards RS. In the first phase of our study, microRNA-19b was identified as a possible target, and in the second phase, we transfected three different CLL cell lines with microRNA-19b mimic and inhibitor and assessed the potential role on leukemia cells in vitro. The mechanism by which miR-19b acts were identified as the upregulation of Ki67 and downregulation of p53. This was further supported through RT-PCR and western blotting on CLL cell lines, as well as by next generation sequencing on two patients diagnosed with CLL that evolved into RS.
IRE1, PERK, and ATF6 are the three transducers of the mammalian canonical unfolded protein response (UPR). GSK2606414 is a potent inhibitor of PERK, while KIRA6 inhibits the kinase activity of IRE1. ...Both molecules are frequently used to probe the biological roles of the UPR in mammalian cells. In a direct binding assay, GSK2606414 bound to the cytoplasmic domain of KIT with dissociation constants (K
) value of 664 ± 294 nM whereas KIRA6 showed a K
value of 10.8 ± 2.9 µM. In silico docking studies confirmed a compact interaction of GSK2606414 and KIRA6 with KIT ATP binding pocket. In cultured cells, GSK2606414 inhibited KIT tyrosine kinase activity at nanomolar concentrations and in a PERK-independent manner. Moreover, in contrast to other KIT inhibitors, GSK2606414 enhanced KIT endocytosis and its lysosomal degradation. Although KIRA6 also inhibited KIT at nanomolar concentrations, it did not prompt KIT degradation, and rescued KIT from GSK2606414-mediated degradation. Consistent with KIT inhibition, nanomolar concentrations of GSK2606414 and KIRA6 were sufficient to induce cell death in a KIT signaling-dependent mast cell leukemia cell line. Our data show for the first time that KIT is a shared target for two seemingly unrelated UPR inhibitors at concentrations that overlap with PERK and IRE1 inhibition. Furthermore, these data underscore discrepancies between in vitro binding measurements of kinase inhibitors and inhibition of the tyrosine kinase receptors in living cells.
The unfolded protein response is an intricate system of sensor proteins in the endoplasmic reticulum (ER) that recognizes misfolded proteins and transmits information via transcription factors to ...either regain proteostasis or, depending on the severity, to induce apoptosis. The main transmembrane sensor is IRE1α, which contains cytoplasmic kinase and RNase domains relevant for its activation and the mRNA splicing of the transcription factor XBP1. Mast cell leukemia (MCL) is a severe form of systemic mastocytosis. The inhibition of IRE1α in the MCL cell line HMC-1.2 has anti-proliferative and pro-apoptotic effects, motivating us to elucidate the IRE1α interactors/regulators in HMC-1.2 cells. Therefore, the TurboID proximity labeling technique combined with MS analysis was applied. Gene Ontology and pathway enrichment analyses revealed that the majority of the enriched proteins are involved in vesicle-mediated transport, protein stabilization, and ubiquitin-dependent ER-associated protein degradation pathways. In particular, the AAA ATPase VCP and the oncoprotein MTDH as IRE1α-interacting proteins caught our interest for further analyses. The pharmacological inhibition of VCP activity resulted in the increased stability of IRE1α and MTDH as well as the activation of IRE1α. The interaction of VCP with both IRE1α and MTDH was dependent on ubiquitination. Moreover, MTDH stability was reduced in IRE1α-knockout cells. Hence, pharmacological manipulation of IRE1α-MTDH-VCP complex(es) might enable the treatment of MCL.
The widespread second messenger molecule cyclic di-GMP (cdG) regulates the transition from motile and virulent lifestyles to sessile, biofilm-forming ones in a wide range of bacteria. Many pathogenic ...and commensal bacterial-host interactions are known to be controlled by cdG signaling. Although the biochemistry of cyclic dinucleotide metabolism is well understood, much remains to be discovered about the downstream signaling pathways that induce bacterial responses upon cdG binding. As part of our ongoing research into the role of cdG signaling in plant-associated Pseudomonas species, we carried out an affinity capture screen for cdG binding proteins in the model organism Pseudomonas fluorescens SBW25. The flagella export AAA+ ATPase FliI was identified as a result of this screen and subsequently shown to bind specifically to the cdG molecule, with a KD in the low micromolar range. The interaction between FliI and cdG appears to be very widespread. In addition to FliI homologs from diverse bacterial species, high affinity binding was also observed for the type III secretion system homolog HrcN and the type VI ATPase ClpB2. The addition of cdG was shown to inhibit FliI and HrcN ATPase activity in vitro. Finally, a combination of site-specific mutagenesis, mass spectrometry, and in silico analysis was used to predict that cdG binds to FliI in a pocket of highly conserved residues at the interface between two FliI subunits. Our results suggest a novel, fundamental role for cdG in controlling the function of multiple important bacterial export pathways, through direct allosteric control of export ATPase proteins.
Background: AAA+ ATPase proteins play integral roles in the export apparatus of many bacterial organelles.
Results: The second messenger cyclic di-GMP binds specifically to multiple export ATPases at a highly conserved binding site.
Conclusion: Cyclic di-GMP binding is central to the function of many different bacterial export complexes.
Significance: This profoundly affects our understanding of numerous important bacterial organelles, including flagella, type III, and type VI secretion systems.
To demonstrate the safety and efficiency of holmium laser-assisted lithotripsy during sialendoscopy of the submandibular gland using a retrospective, interventional consecutive case series.
We ...performed 374 sialendoscopies between 2008 and 2015 and evaluated all patients regarding clinical symptoms, clinical findings, therapy and outcome. We performed 109 procedures of holmium laser-assisted lithotripsy in 64 patients whose sialoliths measured 5 mm or more in diameter. In addition to retrospective case note reviews, we performed telephone interviews of all patients in January 2017.
We performed 374 consecutive submandibular gland sialendoscopy procedures in 276 patients between 2008 to 2015. Sialolithiasis had either previously been diagnosed, or symptoms highly suggestive of sialolithiasis of the submandibular gland presented in 197 patients.
Holmium laser-assisted Laser lithotripsy was performed in 109 cases (64.9%). Smaller mobile concrement was removed directly either by forceps or wire basket, or following marsupialisation of the submandibular duct. This was the case in 88 patients (29.1%). Three patients (0.8%) required surgical removal of the submandibular gland due to early abscess. The majority of patients (n = 374 procedures; 90.1%) remained symptom-free after two or more years following intervention. In the remaining procedures (n = 37 procedures; 9.9%), patients reported discreet postprandial problems but did not seek medical attention. In total, we managed to preserve the submandibular gland and avoid open surgery in 99% of patients through endoscopic management of submandibular concrement and duct stenosis.
Holmium laser-assisted lithotripsy is a simple, safe, and effective procedure for treating patients with sialolithiasis of the submandibular gland. Removal of the gland is rarely required, and removing the gland without prior sialendoscopy is no longer recommended. It should be offered to all patients with submandibular gland sialolithiasis, or such patients should be referred to the appropriate centre for sialendoscopy before submandibulectomy is considered.
Professional Penetration Testing: Creating and Operating a Formal Hacking Lab examines all aspects of professional penetration testing, from project management to team building, metrics, risk ...management, training, reporting, information gathering, vulnerability identification, vulnerability exploitation, privilege escalation, and test-data archival methods. It also discusses how to maintain access and cover one's tracks. It includes two video courses to teach readers fundamental and intermediate information-system penetration testing techniques, and to explain how to create and operate a formal hacking lab.The book is divided into three parts. Part 1 focuses on the professionals who are members of a penetration test team, the skills required to be an effective team member, and the ways to create a PenTest lab. Part 2 looks at the activities involved in a penetration test and how to run a PenTest to improve the overall security posture of the client. Part 3 discusses the creation of a final report for the client, cleaning up the lab for the next penetration test, and identifying the training needs of penetration-test team members. This book will benefit both experienced and novice penetration test practitioners.Find out how to turn hacking and pen testing skills into a professional career Understand how to conduct controlled attacks on a network through real-world examples of vulnerable and exploitable servers Master project management skills necessary for running a formal penetration test and setting up a professional ethical hacking business Discover metrics and reporting methodologies that provide experience crucial to a professional penetration tester
Purpose
The characteristic MRI features of multiple sclerosis (MS) lesions make it conceptually appealing to pursue parametric mapping techniques that support simultaneous generation of quantitative ...maps of 2 or more MR contrast mechanisms. We present a modular rapid acquisition with relaxation enhancement (RARE)‐EPI hybrid that facilitates simultaneous T2 and T2∗ mapping (2in1‐RARE‐EPI).
Methods
In 2in1‐RARE‐EPI the first echoes in the echo train are acquired with a RARE module, later echoes are acquired with an EPI module. To define the fraction of echoes covered by the RARE and EPI module, an error analysis of T2 and T2∗ was conducted with Monte Carlo simulations. Radial k‐space (under)sampling was implemented for acceleration (R = 2). The feasibility of 2in1‐RARE‐EPI for simultaneous T2 and T2∗ mapping was examined in a phantom study mimicking T2 and T2∗ relaxation times of the brain. For validation, 2in1‐RARE‐EPI was benchmarked versus multi spin‐echo (MSE) and multi gradient‐echo (MGRE) techniques. The clinical applicability of 2in1‐RARE‐EPI was demonstrated in healthy subjects and MS patients.
Results
There was a good agreement between T2/T2∗ values derived from 2in1‐RARE‐EPI and T2/T2∗ reference values obtained from MSE and MGRE in both phantoms and healthy subjects. In patients, MS lesions in T2 and T2∗ maps deduced from 2in1‐RARE‐EPI could be just as clearly delineated as in reference maps calculated from MSE/MGRE.
Conclusion
This work demonstrates the feasibility of radially (under)sampled 2in1‐RARE‐EPI for simultaneous T2 and T2∗ mapping in MS patients.
PDF
