1,340 research outputs found
Crime and Punishment Around the World
No full textIt is a subject as old as civil society, yet one that still fuels debate. Now the many and varied aspects of that subject are brought together in the four-volume Crime and Punishment around the World. This unprecedented work provides descriptions of crimes--and the justice systems that define and punish them--in more than 200 nations, principalities, and dependencies.
Each chapter examines the historical, political, and cultural background, as well as the basic organization of the subject state's legal and criminal justice system. It also reports on the types and levels of crime, the processes leading to the finding of guilt, the rights of the accused, alternatives to going to trial, how suspects are prosecuted for their crimes, and the techniques and conditions of typical punishments employed. Comprising a study that is at once extraordinarily comprehensive and minutely detailed, the essays collected here showcase the variety and the universality of crime and punishment the world over. 1. Africa and the Middle East / Mahesh K. Nalla --
2. The Americas / Janet P. Stamatel and Hung-En Sung --
3. Asia and Pacific / Doris C. Chu --
4. Europe / Marcelo F. Aebi and Vřonique Jaquier
Overplaying the role of honey bees as pollinators:a comment on Aebi and Neumann (2011)
No full textletter in response to Aebi and Neumann (2011
Promoter analysis of cgl2, a galectin encoding gene transcribed during fruiting body formation in Coprinopsis cinerea (Coprinus cinereus)
No full textIn the homobasidiomycete Coprinopsis cinerea, expression of the two fruiting body-specific galectins, CGLI and CGL2, is controlled by nutrients, light and darkness and the A mating type genes. In this study, we analyzed the promoter of the cgl2 gene by measuring transcript levels by quantitative real-time PCR and show that regulation of CGL2 expression occurs at the transcriptional level. A minimal promoter sufficient to confer regulated expression of a heterologous reporter gene and comprising 627 base pairs from the start codon was defined. On the minimal promoter we identified a 120 bp sequence mediating induction of the Cgl2 gene in constant darkness. Along with direct repeats (TGGAAG/TGGAAG/GGAA), the sequence contains a CRE consensus site (cAMP-responsive element, TGCGTCA) suggesting the involvement of cAMP signaling in cgl2 activation. No specific elements responsible for light repression and mating type regulation were found in the promoter. (C) 2004 Elsevier Inc. All rights reserved
Functional analysis of biological matter across dimensions by atomic force microscopy (AFM): from tissues to molecules and, ultimately, atoms
No full textFor a detailed understanding of biological tissues and proteins and their dynamical processes the 3D structures of the components involved must be known. Most of the structural data have been obtained through the combination of three major techniques: X-ray crystallography, NMR and TEM. These three methods enable the determination of the structure of biological macromolecules at near atomic resolution and each of those was developed over many years to perfection. Nevertheless each one has its advantage and limitations and all of them may be considered today as useful and complementary tools (Schabert and Engel 1995).
In addition to those established techniques, probably the most spectacular advances have been achieved with the AFM, which is the first imaging device allowing direct correlation between structural and functional states of biomolecules in their physiological environment over a range of scaling very much comparable to the capabilities of EM. Moreover, the AFM has the striking possibility to observe biological matter with high resolution in space, time and applied force and with a striking signal-to-noise ratio that typically allows to directly using unprocessed data.
Using time-lapse AFM, it is possible to monitor the structural and conformational changes with various biological processes such as the assembly/ disassembly mechanisms of proteins. The AFM tip can also be used to manipulate and control single molecules with forces in the piconewton range. Two interesting examples are the mechanical unfolding of proteins and the measurement of the actin-myosin interaction force.
Theoretically the AFM enables to image, probe and manipulate biomolecules in a fully native state at submolecular resolution. However, at the moment this is only feasible for reconstituted transmembrane proteins that are forming 2D crystals in vitro. Imaging of a huge variety of other interesting specimens, e.g. DNA, motor proteins, living cells or the sponge like nuclear pore complex, only reveal macromolecular or even a poorer resolution and protocols for investigating and analyzing other types of biological samples, e.g. connective tissues (cartilage, tendon, bone) or the plaque particles in the coronary arteries, so far are not worked out. In this doctoral thesis I refined or developed several new preparation protocols applicable for the investigation on a variety of biological or medical relevant samples:
In a first project we applied high resolution AFM imaging to the luminal and cytoplasmic face of the asymmetric unit membrane (AUM) of the urine bladder epithelium that forms 2D crystalline plaques in vivo. Those urothelial plaques are meant to be involved in a variety of pathological processes, like bladder cancer that ranges among the five most frequent cancer diseases. Moreover, the investigation of AUM in the AFM could offer a basic understanding of the plaque forming process at the innermost part of the bladder, which potentially might also give new insights into a wide variety of structural and dynamical changes occurring in a lipid membrane in situ.
In a second project we succeeded to establish a protocol for the robust immobilization of different assemblies of the water soluble protein actin, a 43-kDa protein that plays a fundamental role in muscle contraction, cytoskeletal processes and motility. We achieved high-resolution AFM images of the G- and F-actin arrays that hold promise for detailed structural analyses at the molecular level of morphological changes induced by chemical effectors. This project aims ultimately to trace the muscle-dynamics in its different conformational steps throughout the ATPase/ cross-bridge cycle and at the level of single molecules, i.e. to trace the mechanical interaction of the molecular motor myosin with actin filaments.
In a third project we developed new preparation and evaluation protocols that should enable us to directly measure the critical biomechanical parameters of soft biological tissue at the micrometer to nanometer scale. Therefore AFM imaging and indentation-based AFM have enabled us to trace alterations of the tissue architecture at all relevant scales. As a first clinically relevant sample we imaged and mechanically tested articular cartilage in its normal state and compared it to a disease state caused by osteoarthritis. These results are paving new vistas for monitoring disease processes at the scale they are actually occurring, i.e. at the cellular to molecular level. Elasticity measurements at different scales on native articular cartilage provided us with a better understanding of cartilage biomechanics and offer new possibilities in mapping cartilage mechanical properties, which will also include the viscoelastic properties in further measurements.
In a next step, individual building blocks were specifically removed out of the tissue architecture by enzyme action. Those digestion experiments helped us to model or mimic alterations caused by pathological degradation processes. At this stage sufficiently smooth samples for high resolution imaging can only be prepared from frozen samples by employing cryo-microtomy. For a refinement of the procedure a protocol has to be developed for combining high resolution imaging with the mechanical probing at the specific sites of interest. Of course the final goal would be that all preparation steps could be done under near physiological conditions.
Concerning clinically relevant applications, this work opens the possibility of an in vivo analysis of cartilage consistence in the knee or the investigation of plaque particles in the coronary arteries. This directly leads to the ultimate goal of in situ force mapping by a minimally invasive procedure, i.e. by incorporating the AFM into an arthroscope or into a heart catheter.
In summary: In the context of structural research in biology and medicine the AFM is a sensitive microscopical technique with exciting new possibilities to explore new areas of revealing interactions of molecules and merging them with those obtained in the related fields of biochemistry and genetics or by different techniques to gain a comprehensive understanding of cell function: motility, organelle dynamics, membrane transport, and regulation. Moreover, it might be very useful to integrate AFM and AFM-based techniques rather than separating the different techniques and disciplines. Structural, genetical and biochemical data might eventually be composed with the intermediate resolution of EM and AFM and atomic resolution achieved by X-ray crystallography and NMR. In a truly integrated approach the AFM should be complementary to – and not competing with – other microscopical techniques, diffraction methods and spectroscopies. The power of AFM is rooted in its unique capabilities of an extremely high dimensional resolution capability and its resolution in applying and/ or measuring forces that potentially allows the tracing of the fundamental biological processes of life, for example, the translocation of mRNA into protein by the ribosome, the production of molecular “fuel” (e.g., ATP) in mitochondria, and the translocation of ions and small molecules across membranes by channels and pumps. Further developments in sample preparation and instrumentation will open up new AFM capabilities in terms of high-resolution imaging, a better temporal resolution in time-lapse imaging, therefore leading to a real-time imaging and a more time efficient force-mapping and maybe a direct data processing.
A higher spatial resolution could be achieved by employing a more sensitive feedback system that requires lower loading forces in combination or in addition to novel and more efficient operational modes, like an improved and more sensitive tapping mode or even better, a real non-contact mode in liquid.
Currently new AFMs are designed that are specialized for faster recording of data (Ando et al. 2001; Viani et al. 1999). These instruments operate shorter cantilevers with low-noise characteristics that respond much faster than those currently in use. The new design allows much higher image speed for tapping mode in liquid and also drastically reduces the time for force mapping. Recently a scan rate of up to one frame per second and one to a few minutes for the force mapping have been achieved respectively. This is an important step to trace conformational changes of biological matter in their physiological states and studying the dynamic processes in real time. In combination with more specific software this eventually allows the recording frames at video speed in the future.
As stated in the introduction, AFM does not only provide the “eyes’’ for high resolution imaging but it also provides the “fingers’’ to measure and manipulate matter at the atomic and molecular level. This is of great relevance in the life sciences: Recently it has been demonstrated by dissecting DNA from a particular part of the chromosome that the probe can also be used as a nanoscalpel to dissect fragile biological samples (Thalhammer et al. 1997).
In this context, force-spectroscopy is another dedicated new methodology, which continuously is under development for investigation, the dynamical processes occurring during the unfolding of a biomolecule (Oesterhelt et al. 2000; Rief et al. 2000; Rief et al. 1997). It might be possible to determine forces generated by a biomolecule on the microsecond time scale. A faster and more sensitive force-spectroscopy based on AFM might allow studying biological processes with greater resolution in time and applied force.
By employing IT AFM the tip can be placed directly atop individual structural features to measure its biomechanical properties. In this doctoral thesis I have demonstrated that biomechanical information such as the elastic modulus can be strongly dependent on the experimental scale which is given by the size of the indenter. This could be especially interesting for putative clinical applications, such as obtaining clinical relevant information at fundamentally different levels of tissues architecture. The attainable spatial resolution is directly related to the shape and sharpness of the scanning probe tip. The apex of commercially available tips typically has typical radii of curvature of some nanometers (Czajkowsky et al. 2000) and will improve in the future in terms of sharpness and in reduction of cantilever noise. There may be a practical advantage in using other tips grown in situ onto cantilevers or carbon nanotubes using an electron microscope. Both types of tips possess many unique properties that make them ideal AFM probes. Their high aspect ratio provides faithful imaging of deep trenches, while good resolution is retained due to their nanometer-scale diameter. These geometrical factors also lead to reduce tip-sample adhesion, which therefore might allow a gentler imaging. New types of cantilevers might be more specific in terms of their physical or chemical functioning of the probe or on the other hand biochemically compatible for biomedical applications. Multifunctional cantilevers will provide the extension to a whole set of new experimental opportunities of monitoring possibly a wide range of multiple signals, like voltage, currents of ions or electrons and fluorescently labeled molecules (Engel et al. 1999).
Nanotubes are electrically conductive, which allow their use for the measurements of (surface-) potentials, and they can be modified at their ends with specific chemical or biological groups for high resolution functional imaging. Nanotubes could also be used as nanopipettes for drug delivery or as an electrical conductive tip for measuring local potentials, currents or trafficking of biomolecules across membranes.
Arrays of cantilevers (millipede) are under development that could be used for mechanically probing simultaneously neighboring regions of the specimen. This could allow mapping mechanical properties or imaging of larger regions within a short time or a more reliable diagnosis, i.e. different tissues or the plaques in the coronal arteries involved in heart diseases, all of them with an extremely high interest for medical research and treatment of diseases.
Combined AFM-SNOM (scanning near-field optical microscopy) - probe tips are potentially of great use and can be handled almost like the commonly used AFM probes. SNOM allows the detection of a conventional AFM height image and additionally an optical image with an improved optical resolution of more than one order of magnitude compared to conventional LM. SNOM therefore offers in addition to the topography also corresponding optical information of fluorescently labeled biological features beyond the diffraction limit of conventional light microscopy. One potential application might be the detection of the green fluorescent protein expressed by some cell strains. These tips can either be used as a detector to follow for example the specimen of green fluorescent proteins or as an effector to induce photoactive processes at the single molecule level.
One of our future projects is to detect the bidirectional trafficking through the nuclear pore complex by fluorescently labeled cargo. To achieve this we are developing a protocol to tightly seal the nuclear envelope of Xenopus oozytes over microfabricated pores. The goal is to measure in their complete functional state the transport rates of these nuclear gates at the level of single pores. In a comparison with genetically modified pores we aim to understand the regulation of cargoes between the nucleus and cytoplasm. The impacts of nano science in medically relevant applications foster the development of new devices and analytical tools for clinical practice. Due to the very high signal-to-noise ratio, AFM-based techniques offer the observation, probing and characterization of the chemical and mechanical properties of single molecules within a tissue in a physiologically relevant environment. Therefore pathological changes in human tissue can be registered and hopefully cured at an early stage of the disease progression. On the other hand by expanding our ability to characterize and control biological tissue in much more detail diagnostics and therapeutics could be revolutionized in terms of delivery of drugs in small amounts with a high resolution to the target.
The new possibilities opened by the AFM will also have an important impact for engineering and (quality-) control of surface properties of new biocompatible implants, tissue-engineered organs or novel biodegradable products that can be resorbed by the body after use. Progress in nanobiotechnology will promote the healing of natural tissue and will stimulate mimicking high-performance biocompatible nanosystems such as artificial active components or biological implants for organ and joint replacement. Thus new implants will be designed with nanoscale features that will replace degenerated, diseased or damaged tissues, e.g. arthritic cartilage or bone.
Since its invention the AFM has opened new avenues for a wide range of exciting applications ranging from basic structural research up to new developments for in situ applications in a clinical environment. However, diseases are often caused largely by damages either at the molecular or the cellular scale. For a local assessment today’s surgical tools are simply too big. In the future we should get tools that are molecular, both in their size and their precision; and then we will be able to intervene directly at the level where the damage occurs and correct it. Ultimately the dream of Richard Feynman and Albert R. Hibbs might become true that once nanoscale machines can be injected into the bloodstream for dialysis or drug delivery
Structure and stability of the Si(331)-(12×1) surface reconstruction investigated with first-principles density functional theory
No full textWe recently proposed a structural model for the Si(331)-(12×1) surface reconstruction containing silicon pentamers and adatoms as elementary structural building blocks. Using first-principles density functional theory we here investigate the stability of a variety of adatom configurations and determine the lowest-energy configuration. We also present a detailed comparison of the energetics between our model for Si(331)-(12×1) and the adatom-tetramer-interstitial model for Si(110)-(16×2), which shares the same structural building blocks
Design and analysis of peptide based nanoparticles
No full textViruses are naturally formed bionanoparticles (BNPs), ranging in size from 22-150 nm. Remarkably, small viruses are composed of one single protein chain folding into a capsid structure with icosahedral symmetry. The icosahedron is built up from 60 asymmetric units and is the largest closed shell in which every subunit is in an identical environment. It is characterized by 2-fold, 3-fold and 5-fold rotational symmetry axes. By superposition of different protein oligomerization domains onto the symmetry axes of the icosahedron, a nanoparticle with icosahedral symmetry can be designed. To test our concept, we have designed a peptide comprising a slightly modified form of a pentameric coiled-coil domain of cartilage oligomeric matrix protein (COMP) linked to a de novo designed trimeric coiled-coil domain as a single chain. These two different oligomeric domains were linked by two glycine residues to provide flexibility between them and were fixed in their relative orientation with an intramolecular disulfide bridge. Computer modeling predicted that such a design would result in an icosahedral peptide based nanoparticle with a diameter of 17 nm. We chemically synthesized the above designed peptide and performed refolding studies and biophysical characterization using analytical ultra centrifugation (AUC) and electron microscopy (EM), thereby showing the formation of icosahedral nanoparticles with a diameter of ~ 17 nm. Subsequently, we switched to recombinant expression of the designed peptide. Again, we performed refolding studies with the expressed peptide and biophysical characterization (AUC and EM), thereby showing the formation of icosahedral nanoparticles with a diameter of ~ 17 nm. In addition, we showed that during refolding, parameters such as ionic strength, pH of the refolding buffer and presence of glycerol influence the formation of icosahedral nanoparticles. Moreover, we observed icosahedral nanoparticles in conditions in which the formation of intramolecular disulfide bridges is not possible. This showed that even in the absence of intramolecular disulfide bridge the helices of the two different oligomeric domains like to be arranged close to each other, as this will favor the formation of icosahedral nanoparticles.
In parallel, we also modified the designed peptide to include charged residues at the
interface between the two oligomeric domains. The idea was to fix the relative orientation
between the two oligomeric domains through ionic interactions. The subsequent
expression, refolding studies and biophysical characterization showed the formation of
nanoparticles, but they were lacking icosahedral symmetry. This result showed that the
design has to be optimized further to obtain icosahedral nanoparticles.
Moreover, we wanted to study whether in our design principles oligomerization motifs
other than coiled-coils can be used to form icosahedral nanoparticles. Accordingly, we
used globular foldon domain as the trimerization domain and the COMP as the
pentamerization domain. The results showed the formation of nanoparticles, but they
were lacking icosahedral symmetry. In addition, in the above design we studied the effect
of linker region by increasing the liker region to four and six residues, but it did not help
in the formation of icosahedral nanoparticles. However, when the foldon domain
extended with the trimeric coiled-coil domain as a single trimerization domain and with
COMP as the penatmerization domain, we observed icosahedral nanoparticles.
Viruses are known for their induction of strong antibody (B-cell) mediated immune
response in the host even against the self-antigens. This property is conferred by the
repetitive arrangement of the antigens on their surface. Peptide based nanoparticles have
similar properties to viruses, such as self-assembly and most importantly the repetitive
arrangement of subunits (peptide based nanoparticles are composed of 60 identical
monomeric chains). Therefore, we wanted to use our system as a ‘repetitive antigen
display carrier’ in vaccination, as an alternative to viral and viral based platforms such as
virus like particles (VLPs). To this end, and in order to understand the effect of our
nanoparticle size on immune response, we built different constructs displaying the pilin
epitope of Pseudomonas pathogen at their C-terminus. Computer modeling indicated that
these constructs would form icosahedral nanoparticles of three sizes: small (18 nm),
medium (23 nm) and large (29 nm). From the refolding studies, we observed mostly
aggregation and precipitation of the nanoparticles.
This effect presumably due to interparticle cross-linking, by the cysteine residues of
pilin epitope which are present at the periphery of nanoparticles, as we observed
aggregation of small size icosahedral nanoparticles upon changing from reducing to
oxidizing condition. Immunization results, because of the aggregation and precipitation
behavior of nanoparticles, showed poor immune response. However, the immunization
results showed that our nanoparticles present the attached epitope in their native form, as
we observed binding against native pilin protein. Moreover, immunization results from
our laboratory using medium size nanoparticles displaying Salmonella epitope D2
showed promising results, as we got antibody titer values which were well comparable to
the values obtained with VLPs. This places our system alongside with VLPs, which are in
clinical trials as a carrier in vaccination
Multiple Colonization with S. pneumoniae before and after Introduction of the Seven-Valent Conjugated Pneumococcal Polysaccharide Vaccine
No full textBackground: Simultaneous carriage of more than one strain of Streptococcus pneumoniae promotes horizontal gene
transfer events and may lead to capsule switch and acquisition of antibiotic resistance. We studied the epidemiology of cocolonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal vaccine(PCV7).
Methodology: Nasopharyngeal swabs (n 1120) were collected from outpatients between 2004 and 2009 within an ongoing
nationwide surveillance program. Cocolonization was detected directly from swabs by restriction fragment length
polymorphism (RFLP) analysis. Serotypes were identified by agglutination, multiplex PCR and microarray.
Principal Findings: Rate of multiple colonization remained stable up to three years after PCV7 introduction. Cocolonization was associated with serotypes of low carriage prevalence in the prevaccine era. Pneumococcal colonization density was higher in cocolonized samples and cocolonizing strains were present in a balanced ratio (median 1.38). Other characteristics of cocolonization were a higher frequency at young age, but no association with recurrent acute otitis media, recent antibiotic exposure, day care usage and PCV7 vaccination status.
Conclusions: Pneumococcal cocolonization is dominated by serotypes of low carriage prevalence in the prevaccine era,
which coexist in the nasopharynx. Emergence of such previously rare serotypes under vaccine selection pressure may promote cocolonization in the future
Assessment of residency program outcomes via alumni surveys
No full textSonja Lüer, Christoph Aebi Department of Pediatrics, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland Background: One trend in medical education is outcomes-oriented training. Outcomes usually refer to individuals’ acquisition of competencies, for example, during training in residency programs. However, little is known about outcomes of these programs. In order to fill this gap, human resource (HR) data were analyzed and alumni of a pediatric residency program were surveyed at the Department of Pediatrics, Bern University Hospital, Switzerland.Methods: Residency program outcomes (demographics, career choices, part-time or full-time work status, competencies, feedback) were assessed through in-house HR databases, publicly available data on the Internet (physician directory and practice homepages), and 2 alumni surveys (S1, S2). Results: In all, 109 alumni met the inclusion criteria. Retention rate at the hospital was low (14%). Forty-six alumni (42%) in private practice were eligible for alumni surveys. Response rates were 87% (S1) and 61% (S2). Time intervals between 2 career decisions (selecting specialty of pediatrics vs selecting setting of private practice) varied widely (late-training decision to enter private practice). Mean employment level in private practice was 60% (range 20%–100%). Most valued rotation was emergency medicine; most desired competencies in future colleagues were the ability to work in a team, proficiency in pediatrics, and working economically.Conclusion: A broadened view on outcomes – beyond individuals’ competency acquisition – provides informative insights into a training program, can allow for informed program updates, and guide future program development. Keywords: medical education, career choice, pediatrics, private practic
Molecular architecture of the yeast nuclear pore complex: Localization of Nsp1p subcomplexes
No full textinfo:eu-repo/semantics/publishe
The dynamics of the Brazilian income
No full textThis paper aims to measure the degree of income mobility in Brazil in the 1987-2005 period. To achieve that, we consider the axiomatic mobility approach and the dynamic tool suggested by Aebi et al. (1999). The transition probability matrix calculations and the mobility index indicate that Brazil has low intragenerational income mobility, suggesting that Brazilian social structure is relatively rigid.Income mobility; Transition probability matrix; Mobility indices
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