OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

High-speed rotational atherectomy before paclitaxel-eluting stent implantation in complex calcified coronary lesions: the randomized ROTAXUS (Rotational Atherectomy Prior to Taxus Stent Treatment for Complex Native Coronary Artery Disease) trial

OBJECTIVES This study sought to determine the effect of rotational atherectomy (RA) on drug-eluting stent (DES) effectiveness. BACKGROUND DES are frequently used in complex lesions, including calcified stenoses, which may challenge DES delivery, expansion, and effectiveness. RA can adequately modify calcified plaques and facilitate stent delivery and expansion. Its impact on DES effectiveness is widely unknown. METHODS The ROTAXUS (Rotational Atherectomy Prior to TAXUS Stent Treatment for Complex Native Coronary Artery Disease) study randomly assigned 240 patients with complex calcified native coronary lesions to RA followed by stenting (n = 120) or stenting without RA (n = 120, standard therapy group). Stenting was performed using a polymer-based slow-release paclitaxel-eluting stent. The primary endpoint was in-stent late lumen loss at 9 months. Secondary endpoints included angiographic and strategy success, binary restenosis, definite stent thrombosis, and major adverse cardiac events at 9 months. RESULTS Despite similar baseline characteristics, significantly more patients in the standard therapy group were crossed over (12.5% vs. 4.2%, p = 0.02), resulting in higher strategy success in the rotablation group (92.5% vs. 83.3%, p = 0.03). At 9 months, in-stent late lumen loss was higher in the rotablation group (0.44 ± 0.58 vs. 0.31 ± 0.52, p = 0.04), despite an initially higher acute lumen gain (1.56 ± 0.43 vs. 1.44 ± 0.49 mm, p = 0.01). In-stent binary restenosis (11.4% vs. 10.6%, p = 0.71), target lesion revascularization (11.7% vs. 12.5%, p = 0.84), definite stent thrombosis (0.8% vs. 0%, p = 1.0), and major adverse cardiac events (24.2% vs. 28.3%, p = 0.46) were similar in both groups. CONCLUSIONS Routine lesion preparation using RA did not reduce late lumen loss of DES at 9 months. Balloon dilation with only provisional rotablation remains the default strategy for complex calcified lesions before DES implantation.

Allelopathic effects of three plant invaders on germination of native species: a field study

The ability of some invasive plant species to produce biochemical compounds toxic to native species, called allelopathy, is thought to be one of the reasons for their success when introduced to a novel range, an idea known as the Novel Weapons Hypothesis. However, support for this hypothesis mainly comes from bioassays and experiments conducted under controlled environments, whereas field evidence is rare. In a field experiment, we investigated whether three plant species invasive in Europe, Solidago gigantea, Impatiens glandulifera and Erigeron annuus, inhibit the germination of native species through allelopathy more than an adjacent native plant community. At three sites for each invasive species, we compared the germination of native species that were sown on invaded and non-invaded plots. Half of these plots were amended with activated carbon to reduce the influence of potential allelopathic compounds. The germination of sown seeds and of seeds from the seedbank was monitored over a period of 9 weeks. Activated carbon generally enhanced seed germination. This effect was equally pronounced in invaded and adjacent non-invaded plots, indicating that invasive species do not suppress germination more than a native plant community. In addition, more seeds germinated from the seedbank on invaded than on non-invaded soil, probably due to previous suppression of germination by the invasive species. Our field study does not provide evidence for the Novel Weapons Hypothesis with respect to the germination success of natives. Instead, our results suggest that if invasive species release allelopathic compounds that suppress germination, they do so to a similar degree as the native plant community.

A Comparison of Complications in 400 Patients After Native Nail Versus Silicone Nail Splints for Fingernail Splinting After Injuries

BACKGROUND The fingertip is the most commonly injured part of the hand and is an important aesthetic part of the hand. METHODS In this retrospective study we analyzed data from 700 patients operated on between 1997 and 2008 for complications after nail splinting with native nail or silicone nail. Inclusion criteria were patients living in Bern/Berner Land, complete documentation, same surgical team, standard antibiotics, acute trauma, no nail bed transplantation, and no systemic diseases. Groups were analyzed for differences in age, gender, cause and extension of trauma, bony injury and extent, infection, infectious agent, and nail deformities. Statistical analysis was done using the χ (2) test, Fisher's exact test, and Pearson correlation coefficients. RESULTS A total of 401 patients, with a median age of 39.5 years, were included. There were more men with injured nails. Two hundred forty native nails and 161 silicone splints were used. There were 344 compression injuries, 44 amputations, and 13 avulsion injuries. Forty-three patients had an infection, with gram-positive bacteria (Staphylococcus aureus) causing most infections. A total of 157 nail dystrophies were observed, split nails most often. The native nail splint group showed significantly (p < 0.015) fewer nail deformities than the silicone nail splint group; otherwise, there were no statistical differences. However, there were twice as many infections in the silicone nail group. CONCLUSION It seems to be advantageous to use the native nail for splinting after trauma, when possible. In case of a destroyed and unusable nail plate, a nail substitute has to be used.

Non-naturalized alien plants receive fewer flower visits than naturalized and native plants in a Swiss botanical garden

Many animal-pollinated plant species have been introduced to non-native regions without their usual pollinators. Nevertheless, some of these alien species managed to establish reproducing naturalized populations, which might negatively affect native plants. Recent studies have shown that many naturalized alien species can readily attract native pollinators. However, it is not known whether alien species that have not established naturalized populations are less successful in attracting pollinators. Therefore, we tested whether flower-visitation rates are lower for non-naturalized aliens than for naturalized alien and native species. We conducted a comparative study on flower visitation of 185 native, 37 naturalized alien and 224 non-naturalized alien plant species in the Botanical Garden of Bern, Switzerland. Our phylogenetically corrected analyses showed that non-naturalized alien species received fewer flower visitors than both naturalized alien and native species. Native, naturalized alien and non-naturalized alien species were visited by similar flower-visitor communities. Furthermore, among the naturalized alien species, the ones with a broader distribution range in Switzerland received a more diverse set of flower visitors. Although it has been suggested that most alien plants can readily integrate into native plant–pollinator networks, we show evidence that the capacity to attract flower visitors in non-native regions is different for naturalized and non-naturalized alien plants. Therefore, we conclude that successful naturalization of alien plants may be related to flower visitation.

Incidence and Imaging Outcomes of Acute Scaffold Disruption and Late Structural Discontinuity After Implantation of the Absorb Everolimus-Eluting Fully Bioresorbable Vascular Scaffold: Optical Coherence Tomography Assessment in the ABSORB Cohort B Trial (A Clinical Evaluation of the Bioabsorbable Everolimus Eluting Coronary Stent System in the Treatment of Patients With De Novo Native Coronary Artery Lesions).

OBJECTIVES This study sought to describe the frequency and clinical impact of acute scaffold disruption and late strut discontinuity of the second-generation Absorb bioresorbable polymeric vascular scaffolds (Absorb BVS, Abbott Vascular, Santa Clara, California) in the ABSORB (A Clinical Evaluation of the Bioabsorbable Everolimus Eluting Coronary Stent System in the Treatment of Patients With De Novo Native Coronary Artery Lesions) cohort B study by optical coherence tomography (OCT) post-procedure and at 6, 12, 24, and 36 months. BACKGROUND Fully bioresorbable scaffolds are a novel approach to treatment for coronary narrowing that provides transient vessel support with drug delivery capability without the long-term limitations of metallic drug-eluting stents. However, a potential drawback of the bioresorbable scaffold is the potential for disruption of the strut network when overexpanded. Conversely, the structural discontinuity of the polymeric struts at a late stage is a biologically programmed fate of the scaffold during the course of bioresorption. METHODS The ABSORB cohort B trial is a multicenter single-arm trial assessing the safety and performance of the Absorb BVS in the treatment of 101 patients with de novo native coronary artery lesions. The current analysis included 51 patients with 143 OCT pullbacks who underwent OCT at baseline and follow-up. The presence of acute disruption or late discontinuities was diagnosed by the presence on OCT of stacked, overhung struts or isolated intraluminal struts disconnected from the expected circularity of the device. RESULTS Of 51 patients with OCT imaging post-procedure, acute scaffold disruption was observed in 2 patients (3.9%), which could be related to overexpansion of the scaffold at the time of implantation. One patient had a target lesion revascularization that was presumably related to the disruption. Of 49 patients without acute disruption, late discontinuities were observed in 21 patients. There were no major adverse cardiac events associated with this finding except for 1 patient who had a non-ischemia-driven target lesion revascularization. CONCLUSIONS Acute scaffold disruption is a rare iatrogenic phenomenon that has been anecdotally associated with anginal symptoms, whereas late strut discontinuity is observed in approximately 40% of patients and could be viewed as a serendipitous OCT finding of a normal bioresorption process without clinical implications. (ABSORB Clinical Investigation, Cohort B [ABSORB B]; NCT00856856).

SNARE-fusion mediated insertion of membrane proteins into native and artificial membranes

Membrane proteins carry out functions such as nutrient uptake, ATP synthesis or transmembrane signal transduction. An increasing number of reports indicate that cellular processes are underpinned by regulated interactions between these proteins. Consequently, functional studies of these networks at a molecular level require co-reconstitution of the interacting components. Here, we report a SNARE protein-based method for incorporation of multiple membrane proteins into artificial membrane vesicles of well-defined composition, and for delivery of large water-soluble substrates into these vesicles. The approach is used for in vitro reconstruction of a fully functional bacterial respiratory chain from purified components. Furthermore, the method is used for functional incorporation of the entire F1F0 ATP synthase complex into native bacterial membranes from which this component had been genetically removed. The novel methodology offers a tool to investigate complex interaction networks between membrane-bound proteins at a molecular level, which is expected to generate functional insights into key cellular functions.

SNARE-fusion mediated inserton of membrane proteins into native and artificial membranes

Membrane proteins carry out functions such as nutrient uptake, ATP synthesis or transmembrane signal transduction. An increasing number of reports indicate that cellular processes are underpinned by regulated interactions between these proteins. Consequently, functional studies of these networks at a molecular level require co-reconstitution of the interacting components. Here, we report a SNARE-protein based method for incorporation of multiple membrane proteins into membranes, and for delivery of large water-soluble substrates into closed membrane vesicles. The approach is used for in vitro reconstruction of a fully functional bacterial respiratory chain from purified components. Furthermore, the method is used for functional incorporation of the entire F1F0-ATP synthase complex into native bacterial membranes from which this component had been genetically removed. The novel methodology offers a tool to investigate complex interaction networks between membrane-bound proteins at a molecular level, which is expected to generate functional insights into key cellular functions.

3D morphometry using automated aortic segmentation in native MR angiography: an alternative to contrast enhanced MRA?

INTRODUCTION Native-MR angiography (N-MRA) is considered an imaging alternative to contrast enhanced MR angiography (CE-MRA) for patients with renal insufficiency. Lower intraluminal contrast in N-MRA often leads to failure of the segmentation process in commercial algorithms. This study introduces an in-house 3D model-based segmentation approach used to compare both sequences by automatic 3D lumen segmentation, allowing for evaluation of differences of aortic lumen diameters as well as differences in length comparing both acquisition techniques at every possible location. METHODS AND MATERIALS Sixteen healthy volunteers underwent 1.5-T-MR Angiography (MRA). For each volunteer, two different MR sequences were performed, CE-MRA: gradient echo Turbo FLASH sequence and N-MRA: respiratory-and-cardiac-gated, T2-weighted 3D SSFP. Datasets were segmented using a 3D model-based ellipse-fitting approach with a single seed point placed manually above the celiac trunk. The segmented volumes were manually cropped from left subclavian artery to celiac trunk to avoid error due to side branches. Diameters, volumes and centerline length were computed for intraindividual comparison. For statistical analysis the Wilcoxon-Signed-Ranked-Test was used. RESULTS Average centerline length obtained based on N-MRA was 239.0±23.4 mm compared to 238.6±23.5 mm for CE-MRA without significant difference (P=0.877). Average maximum diameter obtained based on N-MRA was 25.7±3.3 mm compared to 24.1±3.2 mm for CE-MRA (P<0.001). In agreement with the difference in diameters, volumes obtained based on N-MRA (100.1±35.4 cm(3)) were consistently and significantly larger compared to CE-MRA (89.2±30.0 cm(3)) (P<0.001). CONCLUSIONS 3D morphometry shows highly similar centerline lengths for N-MRA and CE-MRA, but systematically higher diameters and volumes for N-MRA.

The association between in-stent neoatherosclerosis and native coronary artery disease progression: a long-term angiographic and optical coherence tomography cohort study.

AIMS The purpose of the present study was to investigate the relationship between in-stent neoatherosclerosis (NA) and native atherosclerosis progression of untreated coronary segments. METHODS AND RESULTS In-stent NA was assessed by optical coherence tomography (OCT) among patients included in the SIRTAX-LATE OCT study 5 years after drug-eluting stent (DES) (sirolimus-eluting and paclitaxel-eluting stents) implantation. Neoatherosclerosis was defined as the presence of fibroatheroma or fibrocalcific plaque within the neointima of stented segments with a longitudinal extension >1.0 mm. Atherosclerosis progression in untreated native coronary segments was evaluated by serial quantitative coronary angiography (QCA). The change in minimal lumen diameter (MLD) was serially assessed within matched segments at baseline and 5-year angiographic follow-up. The key clinical endpoint was non-target lesion (non-TL) revascularization throughout 5 years. A total of 88 patients with 88 lesions were available for OCT analysis 5 years after DES implantation. In-stent NA was observed in 16% of lesions with the majority of plaques being fibroatheromas (11.4%) followed by fibrocalcific plaques (5.7%). A total of 704 non-TL segments were serially evaluated by QCA. Between baseline and 5-year follow-up, the reduction in MLD was significantly more pronounced in patients with NA (-0.25 mm, 95% CI -0.36 to -0.17 mm) when compared with patients without NA (-0.13 mm, 95% CI -0.17 to -0.10 mm, P = 0.002). Similarly, non-TL revascularization was more frequent in patients with NA (78.6%) when compared with patients without NA (44.6%, P = 0.028) throughout 5 years. CONCLUSIONS In-stent NA is more common among patients with angiographic and clinical evidence of native atherosclerosis progression suggesting similar pathophysiological mechanisms.SIRTAX trial is registered at http://www.clinicaltrials.gov/ct2/show/NCT00617084.

Dynamics of Traditional Ecological Knowledge, Local Use and Conservation of Native Trees and Shrubs in the Bolivian Andes

Native trees and shrubs are essential components of rural landscapes in the semi-arid inner-Andean valleys of Bolivia. They can be found as hedges and bushes in various agroecosystems such as terrace walls, slopes, field boundaries and fallow land. Their distribution and floristic composition are the result of dynamic spatial and temporal interactions between local farmers and the environment. Local uses of natural resources and biodiversity reflect the constantly evolving Andean culture, which can be generally characterised as an intertwining of the human, natural, and spiritual worlds. The aim of the present ethnobotanical study was to analyse the dynamics of traditional ecological knowledge, to ascertain local farmers’ perceptions and uses of native woody species in Andean communities and to associate the results with local conservation activities for the trees and shrubs concerned. Our case study was carried out within two communities of the Tunari National Park (Dept. Cochabamba) in Bolivia. For data collection, research methods from social science (semi-structured interviews, participative observation, participatory mapping) as well as vegetation surveys were combined. Local actors included women and men of all ages as well as families from different social categories and altitudinal levels of permanent residence. Our study indicates that, due to a multitude of socio-economic pressures (e.g. migration of young people) as well as changes in use of biodiversity (e.g. replacement of native by exotic introduced species), the traditional ecological knowledge base of native trees and shrubs and their respective uses has become diminished over time. In many cases it has led to a decline in people’s awareness of native species and as a consequence their practical, emotional and spiritual relationships with them have been lost. However, results also show that applied traditional ecological knowledge has led to local conservation strategies, which have succeeded in protecting those tree and shrub species which are most widely regarded for their multifunctional, constant and exclusive uses (e.g. Schinus molle, Prosopis laevigata, Baccharis dracunculifolia). The presentation will discuss the question if and how applied traditional ecological knowledge positively contributes to local initiatives of sustainable use and conservation of biodiversity in rural areas.

Inversion, Obviation, and Animacy in Native Languages of the Americas: Elements for a Cross-linguistic Survey

Native languages of the Americas whose predicate and clause structure reflect nominal hierarchies show an interesting range of structural diversity not only with respect to morphological makeup of their predicates and arguments but also with respect to the factors governing obviation status. The present article maps part of such diversity. The sample surveyed here includes languages with some sort of nonlocal (third person acting on third person) direction-marking system.

Visualization of cell microtubules in their native state.

BACKGROUND INFORMATION Over the past decades, cryo-electron microscopy of vitrified specimens has yielded a detailed understanding of the tubulin and microtubule structures of samples reassembled in vitro from purified components. However, our knowledge of microtubule structure in vivo remains limited by the chemical treatments commonly used to observe cellular architecture using electron microscopy. RESULTS We used cryo-electron microscopy and cryo-electron tomography of vitreous sections to investigate the ultrastructure of microtubules in their cellular context. Vitreous sections were obtained from organotypic slices of rat hippocampus and from Chinese-hamster ovary cells in culture. Microtubules revealed their protofilament ultrastructure, polarity and, in the most favourable cases, molecular details comparable with those visualized in three-dimensional reconstructions of microtubules reassembled in vitro from purified tubulin. The resolution of the tomograms was estimated to be approx. 4 nm, which enabled the detection of luminal particles of approx. 6 nm in diameter inside microtubules. CONCLUSIONS The present study provides a first step towards a description of microtubules, in addition to other macromolecular assemblies, in an unperturbed cellular context at the molecular level. As the resolution appears to be similar to that obtainable with plunge-frozen samples, it should allow for the in vivo identification of larger macromolecular assemblies in vitreous sections of whole cells and tissues.

Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state.

The cell envelope of mycobacteria, which include the causative agents of tuberculosis and leprosy, is crucial for their success as pathogens. Despite a continued strong emphasis on identifying the multiple chemical components of this envelope, it has proven difficult to combine its components into a comprehensive structural model, primarily because the available ultrastructural data rely on conventional electron microscopy embedding and sectioning, which are known to induce artifacts. The existence of an outer membrane bilayer has long been postulated but has never been directly observed by electron microscopy of ultrathin sections. Here we have used cryo-electron microscopy of vitreous sections (CEMOVIS) to perform a detailed ultrastructural analysis of three species belonging to the Corynebacterineae suborder, namely, Mycobacterium bovis BCG, Mycobacterium smegmatis, and Corynebacterium glutamicum, in their native state. We provide new information that accurately describes the different layers of the mycobacterial cell envelope and challenges current models of the organization of its components. We show a direct visualization of an outer membrane, analogous to that found in gram-negative bacteria, in the three bacterial species examined. Furthermore, we demonstrate that mycolic acids, the hallmark of mycobacteria and related genera, are essential for the formation of this outer membrane. In addition, a granular layer and a low-density zone typifying the periplasmic space of gram-positive bacteria are apparent in CEMOVIS images of mycobacteria and corynebacteria. Based on our observations, a model of the organization of the lipids in the outer membrane is proposed. The architecture we describe should serve as a reference for future studies to relate the structure of the mycobacterial cell envelope to its function.