How HIV takes advantage of the cytoskeleton in entry and replication

The host cell cytoskeleton plays a key role in the life cycle of viral pathogens whose propagation depends on mandatory intracellular steps. Accordingly, also the human immunodeficiency virus type 1 (HIV-1) has evolved strategies to exploit and modulate in particular the actin cytoskeleton for its purposes. This review will recapitulate recent findings on how HIV-1 hijacks the cytoskeleton to facilitate entry into, transport within and egress from host cells as well as to commandeer communication of infected with uninfected bystander cells.

Early reperfusion hemodynamics predict recovery in rat hearts: a potential approach towards evaluating cardiac grafts from non-heart-beating donors

Aims Cardiac grafts from non-heartbeating donors (NHBDs) could significantly increase organ availability and reduce waiting-list mortality. Reluctance to exploit hearts from NHBDs arises from obligatory delays in procurement leading to periods of warm ischemia and possible subsequent contractile dysfunction. Means for early prediction of graft suitability prior to transplantation are thus required for development of heart transplantation programs with NHBDs. Methods and Results Hearts (n = 31) isolated from male Wistar rats were perfused with modified Krebs-Henseleit buffer aerobically for 20 min, followed by global, no-flow ischemia (32°C) for 30, 50, 55 or 60 min. Reperfusion was unloaded for 20 min, and then loaded, in working-mode, for 40 min. Left ventricular (LV) pressure was monitored using a micro-tip pressure catheter introduced via the mitral valve. Several hemodynamic parameters measured during early, unloaded reperfusion correlated significantly with LV work after 60 min reperfusion (p<0.001). Coronary flow and the production of lactate and lactate dehydrogenase (LDH) also correlated significantly with outcomes after 60 min reperfusion (p<0.05). Based on early reperfusion hemodynamic measures, a composite, weighted predictive parameter, incorporating heart rate (HR), developed pressure (DP) and end-diastolic pressure, was generated and evaluated against the HR-DP product after 60 min of reperfusion. Effective discriminating ability for this novel parameter was observed for four HR*DP cut-off values, particularly for ≥20 *103 mmHg*beats*min−1 (p<0.01). Conclusion Upon reperfusion of a NHBD heart, early evaluation, at the time of organ procurement, of cardiac hemodynamic parameters, as well as easily accessible markers of metabolism and necrosis seem to accurately predict subsequent contractile recovery and could thus potentially be of use in guiding the decision of accepting the ischemic heart for transplantation.

Characterization of MENX-associated pituitary tumours

Aims: The aim of this study is to evaluate the pathological features, serum hormone levels and ex-vivo cultures of pituitary adenomas that occur in rats affected by MENX syndrome. MENX is multiple endocrine neoplasia syndrome caused by a germline mutation in the cell cycle inhibitor p27. Characterisation of MENX adenomas is a prerequisite to exploit this animal model for molecular and translational studies of pituitary adenomas. Methods: We investigated MENX pituitary adenomas with immunohistochemistry, double immunofluorescence, electron microscopy, RT-PCR, measurement of serum hormone levels and ex-vivo cultures. Results: Adenomas in MENX rats belong to the gonadotroph lineage. They start from 4 months of age as multiple neoplastic nodules and progress to become large lesions that efface the gland. Adenomas are composed of chromophobic cells predominantly expressing the glycoprotein alpha-subunit (αGSU). They show mitotic activity and high Ki67 labelling. A few neoplastic cells co-express gonadotrophins and the transcription factor SF1, together with growth hormone or prolactin and Pit-1, suggesting that they are not fully committed to one cell lineage. Ex vivo cultures show features similar to the primary tumour. Conclusions: Our results suggest that p27 function is critical in regulating gonadotroph cells growth. The MENX syndrome represents a unique model to elucidate the physiological and molecular mechanisms mediating the pathogenesis of gonadotroph adenomas. © 2012 The Authors. Neuropathology and Applied Neurobiology © 2012 British Neuropathological Society.

Reduction in Predator Defense in the Presence of Neighbors in a Colonial Fish

Predation pressure has long been considered a leading explanation of colonies, where close neighbors may reduce predation via dilution, alarming or group predator attacks. Attacking predators may be costly in terms of energy and survival, leading to the question of how neighbors contribute to predator deterrence in relationship to each other. Two hypotheses explaining the relative efforts made by neighbors are byproduct-mutualism, which occurs when breeders inadvertently attack predators by defending their nests, and reciprocity, which occurs when breeders deliberately exchange predator defense efforts with neighbors. Most studies investigating group nest defense have been performed with birds. However, colonial fish may constitute a more practical model system for an experimental approach because of the greater ability of researchers to manipulate their environment. We investigated in the colonial fish, Neolamprologus caudopunctatus, whether prospecting pairs preferred to breed near conspecifics or solitarily, and how breeders invested in anti-predator defense in relation to neighbors. In a simple choice test, prospecting pairs selected breeding sites close to neighbors versus a solitary site. Predators were then sequentially presented to the newly established test pairs, the previously established stimulus pairs or in between the two pairs. Test pairs attacked the predator eight times more frequently when they were presented on their non-neighbor side compared to between the two breeding sites, where stimulus pairs maintained high attack rates. Thus, by joining an established pair, test pairs were able to reduce their anti-predator efforts near neighbors, at no apparent cost to the stimulus pairs. These findings are unlikely to be explained by reciprocity or byproduct-mutualism. Our results instead suggest a commensal relationship in which new pairs exploit the high anti-predator efforts of established pairs, which invest similarly with or without neighbors. Further studies are needed to determine the scope of commensalism as an anti-predator strategy in colonial animals.

Analyzing, Capturing and Taming Software Change

Software systems need to continuously change to remain useful. Change appears in several forms and needs to be accommodated at different levels. We propose ChangeBoxes as a mechanism to encapsulate, manage, analyze and exploit changes to software systems. Our thesis is that only by making change explicit and manipulable can we enable the software developer to manage software change more effectively than is currently possible. Furthermore we argue that we need new insights into assessing the impact of changes and we need to provide new tools and techniques to manage them. We report on the results of some initial prototyping efforts, and we outline a series of research activities that we have started to explore the potential of ChangeBoxes.

Molecular mechanisms of pathogenicity of Mycoplasma mycoides subsp. mycoides SC

Mycoplasma mycoides subsp. mycoides SC, the aetiological agent of contagious bovine pleuropneumonia (CBPP), is considered the most pathogenic of the Mycoplasma species. Its virulence is probably the result of a coordinated action of various components of an antigenically and functionally dynamic surface architecture. The different virulence attributes allow the pathogen to evade the host's immune defence, adhere tightly to the host cell surface, persist and disseminate in the host causing mycoplasmaemia, efficiently import energetically valuable nutrients present in the environment, and release and simultaneously translocate toxic metabolic pathway products to the host cell where they cause cytotoxic effects that are known to induce inflammatory processes and disease. This strategy enables the mycoplasma to exploit the minimal genetic information in its small genome, not only to fulfil the basic functions for its replication but also to damage host cells in intimate proximity thereby acquiring the necessary bio-molecules, such as amino acids and nucleic acid precursors, for its own biosynthesis and survival.

Visualization and quantitative analysis of nanoparticles in the respiratory tract by transmission electron microscopy

ABSTRACT: Nanotechnology in its widest sense seeks to exploit the special biophysical and chemical properties of materials at the nanoscale. While the potential technological, diagnostic or therapeutic applications are promising there is a growing body of evidence that the special technological features of nanoparticulate material are associated with biological effects formerly not attributed to the same materials at a larger particle scale. Therefore, studies that address the potential hazards of nanoparticles on biological systems including human health are required. Due to its large surface area the lung is one of the major sites of interaction with inhaled nanoparticles. One of the great challenges of studying particle-lung interactions is the microscopic visualization of nanoparticles within tissues or single cells both in vivo and in vitro. Once a certain type of nanoparticle can be identified unambiguously using microscopic methods it is desirable to quantify the particle distribution within a cell, an organ or the whole organism. Transmission electron microscopy provides an ideal tool to perform qualitative and quantitative analyses of particle-related structural changes of the respiratory tract, to reveal the localization of nanoparticles within tissues and cells and to investigate the 3D nature of nanoparticle-lung interactions.This article provides information on the applicability, advantages and disadvantages of electron microscopic preparation techniques and several advanced transmission electron microscopic methods including conventional, immuno and energy-filtered electron microscopy as well as electron tomography for the visualization of both model nanoparticles (e.g. polystyrene) and technologically relevant nanoparticles (e.g. titanium dioxide). Furthermore, we highlight possibilities to combine light and electron microscopic techniques in a correlative approach. Finally, we demonstrate a formal quantitative, i.e. stereological approach to analyze the distributions of nanoparticles in tissues and cells.This comprehensive article aims to provide a basis for scientists in nanoparticle research to integrate electron microscopic analyses into their study design and to select the appropriate microscopic strategy.

Transgenic system for conditional induction and rescue of chronic myocardial hibernation provides insights into genomic programs of hibernation

A key energy-saving adaptation to chronic hypoxia that enables cardiomyocytes to withstand severe ischemic insults is hibernation, i.e., a reversible arrest of contractile function. Whereas hibernating cardiomyocytes represent the critical reserve of dysfunctional cells that can be potentially rescued, a lack of a suitable animal model has hampered insights on this medically important condition. We developed a transgenic mouse system for conditional induction of long-term hibernation and a system to rescue hibernating cardiomyocytes at will. Via myocardium-specific induction (and, in turn, deinduction) of a VEGF-sequestering soluble receptor, we show that VEGF is indispensable for adjusting the coronary vasculature to match increased oxygen consumption and exploit this finding to generate a hypoperfused heart. Importantly, ensuing ischemia is tunable to a level at which large cohorts of cardiomyocytes are driven to enter a hibernation mode, without cardiac cell death. Relieving the VEGF blockade even months later resulted in rapid revascularization and full recovery of contractile function. Furthermore, we show that left ventricular remodeling associated with hibernation is also fully reversible. The unique opportunity to uncouple hibernation from other ischemic heart phenotypes (e.g., infarction) was used to determine the genetic program of hibernation; uncovering hypoxia-inducible factor target genes associated with metabolic adjustments and induced expression of several cardioprotective genes. Autophagy, specifically self-digestion of mitochondria, was identified as a key prosurvival mechanism in hibernating cardiomyocytes. This system may lend itself for examining the potential utility of treatments to rescue dysfunctional cardiomyocytes and reverse maladaptive remodeling.

Livelihoods in Transition: Changing Land Use Strategies and Ecological Implications in a Post Soviet Setting (Kyrgyzstan)

The sudden independence of Kyrgyzstan from the Soviet Union in 1991 led to a total rupture of industrial and agricultural production. Based on empirical data, this study seeks to identify key land use transformation processes since the late 1980s, their impact on people's livelihoods and the implication for natural resources in the communes of Tosh Bulak and Saz, located in the Sokuluk River Basin on the northern slope of the Kyrgyz Range. Using the concept of the sustainable livelihood approach as an analytical framework, three different livelihood strategies were identified: (1) An accumulation strategy applied by wealthy households where renting and/or buying of land is a key element; they are the only household category capable of venturing into rain fed agriculture. (2) A preserving strategy involving mainly intermediate households who are not able to buy or rent additional agricultural land; very often they are forced to return their land to the commune or sell it to wealthier households. (3) A coping strategy including mainly poor households consisting of elderly pensioners or headed by single mothers; due to their limited labour and economic power, agricultural production is very low and hardly covers subsistence needs; pensions and social allowances form the backbone of these livelihoods. Ecological assessments have shown that the forage productivity of remote high mountain pastures has increased from 5 to 22 per cent since 1978. At the same time forage productivity on pre-mountain and mountain pastures close to villages has generally decreased from 1 to 34 per cent. It seems that the main avenues for livelihoods to increase their wealth are to be found in the agricultural sector by controlling more and mainly irrigated land as well as by increasing livestock. The losers in this process are thus those households unable to keep or exploit their arable land or to benefit from new agricultural land. Ensuring access to land for the poor is therefore imperative in order to combat rural poverty and socio-economic disparities in rural Kyrgyzstan.

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.

Strategies to determine the biological function of microRNAs

MicroRNAs (miRNAs) are regulators of gene expression that control many biological processes in development, differentiation, growth and metabolism. Their expression levels, small size, abundance of repetitive copies in the genome and mode of action pose unique challenges in studies elucidating the function of miRNAs. New technologies for identification, expression profiling and target gene validation, as well as manipulation of miRNA expression in vivo, will facilitate the study of their contribution to biological processes and disease. Such information will be crucial to exploit the emerging knowledge of miRNAs for the development of new human therapeutic applications.

Evaluating retraining rules for semi-supervised learning in neural network based cursive word recognition

Training a system to recognize handwritten words is a task that requires a large amount of data with their correct transcription. However, the creation of such a training set, including the generation of the ground truth, is tedious and costly. One way of reducing the high cost of labeled training data acquisition is to exploit unlabeled data, which can be gathered easily. Making use of both labeled and unlabeled data is known as semi-supervised learning. One of the most general versions of semi-supervised learning is self-training, where a recognizer iteratively retrains itself on its own output on new, unlabeled data. In this paper we propose to apply semi-supervised learning, and in particular self-training, to the problem of cursive, handwritten word recognition. The special focus of the paper is on retraining rules that define what data are actually being used in the retraining phase. In a series of experiments it is shown that the performance of a neural network based recognizer can be significantly improved through the use of unlabeled data and self-training if appropriate retraining rules are applied.

Exploiting Runtime Information in the IDE

Developers rely on the mechanisms provided by their IDE to browse and navigate a large software system. These mechanisms are usually based purely on a system's static source code. The static perspective, however, is not enough to understand an object-oriented program's behavior, in particular if implemented in a dynamic language. We propose to enhance IDEs with a program's runtime information (eg. message sends and type information) to support program comprehension through precise navigation and informative browsing. To precisely specify the type and amount of runtime data to gather about a system under development, dynamically and on demand, we adopt a technique known as partial behavioral reflection. We implemented navigation and browsing enhancements to an IDE that exploit this runtime information in a prototype called Hermion. We present preliminary validation of our experimental enhanced IDE by asking developers to assess its usefulness to understand an unfamiliar software system.

Does organic grassland farming benefit plant and arthropod diversity at the expense of yield and soil fertility?

Organic management is one of the most popular strategies to reduce negative environmental impacts of intensive agriculture. However, little is known about benefits for biodiversity and potential worsening of yield under organic grasslands management across different grassland types, i.e. meadow, pasture and mown pasture. Therefore, we studied the diversity of vascular plants and foliage-living arthropods (Coleoptera, Araneae, Heteroptera, Auchenorrhyncha), yield, fodder quality, soil phosphorus concentrations and land-use intensity of organic and conventional grasslands across three study regions in Germany. Furthermore, all variables were related to the time since conversion to organic management in order to assess temporal developments reaching up to 18 years. Arthropod diversity was significantly higher under organic than conventional management, although this was not the case for Araneae, Heteroptera and Auchenorrhyncha when analyzed separately. On the contrary, arthropod abundance, vascular plant diversity and also yield and fodder quality did not considerably differ between organic and conventional grasslands. Analyses did not reveal differences in the effect of organic management among grassland types. None of the recorded abiotic and biotic parameters showed a significant trend with time since transition to organic management, except soil organic phosphorus concentrations which decreased with time. This implies that permanent grasslands respond slower and probably weaker to organic management than crop fields do. However, as land-use intensity and inorganic soil phosphorus concentrations were significantly lower in organic grasslands, overcoming seed and dispersal limitation by re-introducing plant species might be needed to exploit the full ecological potential of organic grassland management. We conclude that although organic management did not automatically increase the diversity of all studied taxa, it is a reasonable and useful way to support agro-biodiversity.

Dose optimization approach to fast X-ray microtomography of the lung alveoli

A basic prerequisite for in vivo X-ray imaging of the lung is the exact determination of radiation dose. Achieving resolutions of the order of micrometres may become particularly challenging owing to increased dose, which in the worst case can be lethal for the imaged animal model. A framework for linking image quality to radiation dose in order to optimize experimental parameters with respect to dose reduction is presented. The approach may find application for current and future in vivo studies to facilitate proper experiment planning and radiation risk assessment on the one hand and exploit imaging capabilities on the other.