A NMR guided approach for CsrA–RNA crystallization

Structure determination of protein–nucleic acid complexes remains a challenging task. Here we present a simple method for generating crystals of a CsrA–nucleic acid complex, guided entirely by results from nuclear magnetic resonances spectroscopy (NMR) spectroscopy. Using a construct that lacks thirteen non-essential C-terminal residues, efficient binding to DNA could be demonstrated. One CsrA dimer interacts with two DNA oligonucleotides, similar to previous findings with RNA. Furthermore, the NMR study of the CsrA–DNA complex was the basis for successfully homing in on conditions that were suitable for obtaining crystals of the CsrA–DNA complex. Our results may be useful for those cases where RNA in protein–nucleic acid complexes may be replaced by DNA.     

QSRA – a quality-value guided de novo short read assembler

Background  

New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data.     

Acquisition of visually guided conditional associative tasks in Göttingen minipigs

Fourteen Göttingen minipigs were trained on two different visually guided conditional associative tasks. In a spatial conditional task, a black stimulus signalled that a response to the left was correct, and a white stimulus signalled that a response to the right was correct. In a conditional go/no-go task, a blue stimulus signalled go, and a red stimulus signalled no-go. The pigs were trained until a behavioural criterion of 90% correct for each of two consecutive sessions. For the spatial conditional task, all pigs reached this criterion in 520 trials or less. For the conditional go/no-go task, all pigs, except three, reached this criterion in 1600 trials or less. Sows and boars learned equally fast. The tasks can be useful for the testing of cognitive function in pig models of human brain disorders.     

Protein–ligand structure guided by backbone and side-chain proton chemical shift perturbations

The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) –5 mM). The determination of the protein–fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for the protein–ligand recognition, and for growing the initial fragment into potent active compounds. The vast majority of fragments are aromatic compounds that induce chemical shift perturbations (CSP) on protein NMR spectra. These experimental CSPs can be quantitatively used to guide the ligand docking, through the comparison between experimental CSPs and CSP back-calculation based on the ring current effect. Here we implemented the CSP back-calculation into the scoring function of the program PLANTS. We compare the results obtained with CSPs measured either on amide or aliphatic protons of the human peroxiredoxin 5. We show that the different kinds of protons lead to different results for resolving the 3D structures of protein–fragment complexes, with the best results obtained with the \(\hbox {H}_{\alpha }\) protons.     

Can random mutation mimic design?: a guided inquiry laboratory for undergraduate students

Complex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results.     

How are humans related to other primates? A guided inquiry laboratory for undergraduate students

Understanding that phylogenies depict the evolutionary history of species is a critical concept for undergraduate biology students. We present an inquiry-based laboratory exercise exploring this concept in the context of the human phylogeny. This activity reinforces several important biological concepts and skills. Bolstered concepts include that evolution is descent with modification, that evolution is a genetic process, and that humans are closely related to apes. In terms of thinking skills, the lab gives students practice with hypothetical-deductive thinking, quantifying patterns from complex data, and evaluating evidence.     

Minimally invasive mapping guided surgical treatment of atrial fibrillation. Utopia or near future?

Isolation of the pulmonary veins has been used as surgical treatment for atrial fibrillation (AF) from the early 90s, as it was incorporated in the Maze procedure. With the evidence that triggers form this area can induce AF, the Maze III procedure has been adapted and modified towards a single lesion around the pulmonary veins for the treatment of paroxysmal and chronic AF in some centers. New ablation techniques with a diversity of energy sources further paved the way for less invasive procedures. Minimal invasive techniques to prevent major surgery may potentially make the treatment available for a patient population that do not have to undergo cardiac surgery for other reasons. Besides these technical developments, high density mapping can be used to identify the AF substrate in the individual patient and optimization of the treatment by local substrate guided ablation. This review aims to summarize the robotic and thoracoscopic techniques to isolate the pulmonary veins. Furthermore, it is discussed why pulmonary veins isolation may be effective in patients with chronic AF, and whether there is a role for mapping guided minimal invasive surgical treatment of AF in the near future.     

Bio-assay guided isolation and identification of α-glucosidase inhibitors from the leaves of Aquilaria sinensis

Eight α-glucosidase inhibitors including four new compounds were isolated from the 70% aqueous ethanolic extract of leaves of Aquilaria sinensis (Lour.) Gilg by activity-directed fractionation and purification processes. The ethanolic extract was first separated into petroleum ether, ethyl acetate, n-butanol and water soluble fractions and screened for inhibitory activity against α-glucosidase. Further activity-directed investigation lead to the isolation of four new compounds with moderate inhibitory activity, viz, aquilarisinin (1), aquilarisin (2), hypolaetin 5-O-β-D-glucuronopyranoside (3) and aquilarixanthone (4) from the n-butanol fraction, and four known compounds showing potent activity including mangiferin (5), iriflophenone 2-O-α-L-rhamnopyranoside (6), iriflophenone 3-C-β-D-glucoside (7) and iriflophenone 3,5-C-β-D-diglucopyranoside (8) from the most potent ethyl acetate fraction. The structures of these compounds were determined by extensive spectroscopic analyses, including IR, UV, ESIMS, HRESIMS, 1D and 2D NMR.     

Chronic Type A aortic dissection: could surgical intervention be guided by molecular markers?

Aortic dissection, occurring following a separation of the layers constituting the complex vascular walls, leads to the formation of a 'false' lumen and disrupts the regulation of aortic wall homeostasis and function. This clinical condition still represents an important health problem and is associated with high mortality. Its natural history mandates surgical intervention when exceeding 55 mm in diameter and involving the ascending portion of the aorta (Type A), on the bases of an anatomical classification dated back to 1965. An intriguing question rising is whether a dissection that overcomes that critic acute phase has still the indication to surgical intervention. Molecular analysis of chronic dissected aortic walls could help in understanding how morphology and structure are affected and whether tissue homeostasis is re-established. Thus, pursued by this consideration, we made a histological and immunohistochemical characterization of a chronic Type A dissection, reporting three major findings: endothelial cells line the aortic primitive lumen, as well as the 'false' one; walls of primitive and 'false' lumina are comparable in thickness; vascular layers in the 'false' lumen are made up of terminally differentiated cells. This evidence obtained in a single specimen encourages a meditation on the compulsory indication for surgical intervention.     

CAD–CAM prosthetically guided bone regeneration using preformed titanium mesh for the reconstruction of atrophic maxillary arches

The protocol presented here is intended to minimise the intervention in bone reconstruction surgery when severe atrophy or deformity is present in the maxillary arches. A patient underwent augmentation of an atrophic maxillary arch using titanium mesh and particulate autogenous plus bovine demineralised bone. After computed tomography data elaboration, computer-aided design and computer-aided machining were used to plan the augmentation of bone volume to improve the implant position needed to support the final dental prosthesis. The augmented maxilla was rapidly prototyped in plastic, and the titanium mesh was tested on this model before the surgical intervention. Then, the preformed titanium mesh was implanted in the maxillary arch with bone grafting. The bone was augmented relative to the position of the implants for the definitive fixed implant-supported rehabilitation. The protocol presented here is a viable, reproducible way to determine the correct bone augmentation for the final implant-supported prosthetic rehabilitation.     

Structure guided P1' modifications of HEA derived β-secretase inhibitors for the treatment of Alzheimer's disease

The synthesis and SAR of a series of BACE-1 hydroxyethyl amine inhibitors containing substitutions on a spirocyclobutyl moiety is described. Selectivity against cathepsin D, a related aspartyl protease with potential off target toxicity, and improved microsomal stability is exemplified.     

Precision IORT – Image guided intraoperative radiation therapy (igIORT) using online treatment planning including tissue heterogeneity correction

BackgroundTo the present date, IORT has been eye and hand guided without treatment planning and tissue heterogeneity correction. This limits the precision of the application and the precise documentation of the location and the deposited dose in the tissue. Here we present a set-up where we use image guidance by intraoperative cone beam computed tomography (CBCT) for precise online Monte Carlo treatment planning including tissue heterogeneity correction.Materials and methodsAn IORT was performed during balloon kyphoplasty using a dedicated Needle Applicator. An intraoperative CBCT was registered with a pre-op CT. Treatment planning was performed in Radiance using a hybrid Monte Carlo algorithm simulating dose in homogeneous (MCwater) and heterogeneous medium (MChet). Dose distributions on CBCT and pre-op CT were compared with each other. Spinal cord and the metastasis doses were evaluated.ResultsThe MCwater calculations showed a spherical dose distribution as expected. The minimum target dose for the MChet simulations on pre-op CT was increased by 40% while the maximum spinal cord dose was decreased by 35%. Due to the artefacts on the CBCT the comparison between MChet simulations on CBCT and pre-op CT showed differences up to 50% in dose.ConclusionsigIORT and online treatment planning improves the accuracy of IORT. However, the current set-up is limited by CT artefacts. Fusing an intraoperative CBCT with a pre-op CT allows the combination of an accurate dose calculation with the knowledge of the correct source/applicator position. This method can be also used for pre-operative treatment planning followed by image guided surgery.