Ion-Exchange Chromatography: Basic Principles and Application.

Ion-exchange chromatography (IEC) is a fractionation technique that allows for the separation of ionizable molecules on the basis of differences in their electrostatic properties. Its large sample-handling capacity, broad applicability (particularly to proteins and enzymes), moderate cost, powerful resolving ability, ability to perform simultaneous quantitation, and ease of scale-up and automation have led to it becoming one of the most versatile and widely used of all liquid chromatography (LC) techniques. In this chapter, we review the basic principles of IEC, as well as the broader criteria for selecting IEC conditions. By way of further illustration, we outline basic laboratory protocols to partially purify a soluble serine peptidase from bovine whole brain tissue, covering crude tissue extract preparation through to partial purification of the target enzyme using a form of IEC, namely, anion-exchange chromatography. Protocols for assaying total protein and enzyme activity in both pre- and post-IEC fractions are also described.

Immunoprecipitation: Variations, Considerations, and Applications.

Immunoprecipitation (IP) refers to methods of affinity chromatography that enrich and/or purify a specific protein from a complex mixture using a specific antibody immobilized on a solid support. Several operations and processes that are dependent on the isolation, concentration, and modification of proteins have seen improvement in their selectivity and separation based on the integration of IP-specific reactions into their workflows. This relatively simple principle has contributed significantly to our understanding of proteins and their behaviors and has become increasingly fundamental to most protein characterization studies today. In this chapter, we review the basic principles of IP and the several factors that influence each stage, and subsequently the success, of an IP experiment. Moreover, variations in application of the IP principle are discussed, and the adaptability of the techniques based on such is highlighted in the provision of two IP workflows to purify a particular protein from an entire cellular proteosome. These workflows cover the preparation and fractionation of crude cellular lysate into individual subcellular fractions, through to both "batch" and "column"-based extractions of the target protein of interest. Protocols for determining the validity of the workflows, and the presence/abundance of the protein of interest, are also briefly described.

COMP-Ang1: Therapeutic potential of an engineered Angiopoietin-1 variant.

The Angiopoietin-1/2 system is an opportune target for therapeutic intervention in a wide range of vascular pathologies, particularly through its association with endothelium. The complex multi-domain structure of native human Angiopoietin-1 has hindered its widespread applicability as a therapeutic agent, prompting the search for alternative approaches to mimicking the Ang1:Tie2 signalling axis; a system with highly complex patterns of regulation involving multiple structurally similar molecules. An engineered variant, Cartilage Oligomeric Matrix Protein - Angiopoietin-1 (COMP-Ang1), has been demonstrated to overcome the limitations of the native molecule and activate the Tie2 pathway with several fold greater potency than Ang1, both in vitro and in vivo. The therapeutic efficacy of COMP-Ang1, at both the vascular and systemic levels, is evident from multiple studies. Beneficial impacts on skeletal muscle regeneration, wound healing and angiogenesis have been reported alongside renoprotective, anti-hypertensive and anti-inflammatory effects. COMP-Ang1 has also demonstrated synergy with other compounds to heighten bone repair, has been leveraged for potential use as a co-therapeutic for enhanced targeted cancer treatment, and has received considerable attention as an anti-leakage agent for microvascular diseases like diabetic retinopathy. This review examines the vascular Angiopoietin:Tie2 signalling mechanism, evaluates the potential therapeutic merits of engineered COMP-Ang1 in both vascular and systemic contexts, and addresses the inherent translational challenges in moving this potential therapeutic from bench-to-bedside.

TRAIL inhibits oxidative stress in human aortic endothelial cells exposed to pro-inflammatory stimuli.

Studies suggest that tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has vasoprotective potential, as low levels of TRAIL cause accelerated vascular calcification, whereas exogenous TRAIL administration exhibits anti-atherosclerotic activity. The mechanism of TRAIL-mediated vasoprotection remains unclear. We studied the effects of TRAIL (100 ng/ml) on human aortic endothelial cells (HAECs) exposed to pro-atherogenic conditions; (a) oscillatory shear stress (±10 dynes/cm2 ) using the ibidi µ-slide fluidic system; (b) pro-inflammatory injury, that is, tumor necrosis factor alpha (TNF-α, 100 ng/ml) and hyperglycemia (30 mM d-glucose). End-points examined included inflammatory gene expression and reactive oxygen species (ROS) formation. TRAIL shifted the net gene expression toward an antioxidant phenotype in HAECs exposed to oscillatory shear stress. TRAIL significantly reduced ROS formation in HAECs exposed to both TNF-α and hyperglycemia. Therefore, TRAIL appears to confer atheroprotective effects on the endothelium, at least in part, by reducing oxidative stress.

Effects of Dutch livestock production on human health and the environment.

Observed multiple adverse effects of livestock production have led to increasing calls for more sustainable livestock production. Quantitative analysis of adverse effects, which can guide public debate and policy development in this area, is limited and generally scattered across environmental, human health, and other science domains. The aim of this study was to bring together and, where possible, quantify and aggregate the effects of national-scale livestock production on 17 impact categories, ranging from impacts of particulate matter, emerging infectious diseases and odor annoyance to airborne nitrogen deposition on terrestrial nature areas and greenhouse gas emissions. Effects were estimated and scaled to total Dutch livestock production, with system boundaries including feed production, manure management and transport, but excluding slaughtering, retail and consumption. Effects were expressed using eight indicators that directly express Impact in the sense of the Drivers-Pressures-State-Impact-Response framework, while the remaining 14 express Pressures or States. Results show that livestock production may contribute both positively and negatively to human health with a human disease burden (expressed in disability-adjusted life years) of up to 4% for three different health effects: those related to particulate matter, zoonoses, and occupational accidents. The contribution to environmental impact ranges from 2% for consumptive water use in the Netherlands to 95% for phosphorus transfer to soils, and extends beyond Dutch borders. While some aggregation across impact categories was possible, notably for burden of disease estimates, further aggregation of disparate indicators would require normative value judgement. Despite difficulty of aggregation, the assessment shows that impacts receive a different contribution of different animal sectors. While some of our results are country-specific, the overall approach is generic and can be adapted and tuned according to specific contexts and information needs in other regions, to allow informed decision making across a broad range of impact categories.

Development of dynamic cell and organotypic skin models, for the investigation of a novel visco-elastic burns treatment using molecular and cellular approaches.

BACKGROUND: Burn injuries are a major cause of morbidity and mortality worldwide. Despite advances in therapeutic strategies for the management of patients with severe burns, the sequelae are pathophysiologically profound, up to the systemic and metabolic levels. Management of patients with a severe burn injury is a long-term, complex process, with treatment dependent on the degree and location of the burn and total body surface area (TBSA) affected. In adverse conditions with limited resources, efficient triage, stabilisation, and rapid transfer to a specialised intensive care burn centre is necessary to provide optimal outcomes. This initial lag time and the form of primary treatment initiated, from injury to specialist care, is crucial for the burn patient. This study aims to investigate the efficacy of a novel visco-elastic burn dressing with a proprietary bio-stimulatory marine mineral complex (MXC) as a primary care treatment to initiate a healthy healing process prior to specialist care. METHODS: A new versatile emergency burn dressing saturated in a >90% translucent water-based, sterile, oil-free gel and carrying a unique bio-stimulatory marine mineral complex (MXC) was developed. This dressing was tested using LabSkin as a burn model platform. LabSkin a novel cellular 3D-dermal organotypic full thickness human skin equivalent, incorporating fully-differentiated dermal and epidermal components that functionally models skin. Cell and molecular analysis was carried out by in vitro Real-Time Cellular Analysis (RTCA), thermal analysis, and focused transcriptomic array profiling for quantitative gene expression analysis, interrogating both wound healing and fibrosis/scarring molecular pathways. In vivo analysis was also performed to assess the bio-mechanical and physiological effects of this novel dressing on human skin. RESULTS: This hybrid emergency burn dressing (EBD) with MXC was hypoallergenic, and improved the barrier function of skin resulting in increased hydration up to 24 h. It was demonstrated to effectively initiate cooling upon application, limiting the continuous burn effect and preventing local tissue from damage and necrosis. xCELLigence RTCA® on primary human dermal cells (keratinocyte, fibroblast and micro-vascular endothelial) demonstrated improved cellular function with respect to tensegrity, migration, proliferation and cell-cell contact (barrier formation) [1]. Quantitative gene profiling supported the physiological and cellular function finding. A beneficial quid pro quo regulation of genes involved in wound healing and fibrosis formation was observed at 24 and 48 h time points. CONCLUSION: Utilisation of this EBD + MXC as a primary treatment is an effective and easily applicable treatment in cases of burn injury, proving both a cooling and hydrating environment for the wound. It regulates inflammation and promotes healing in preparation for specialised secondary burn wound management. Moreover, it promotes a healthy remodelling phenotype that may potentially mitigate scarring. Based on our findings, this EBD + MXC is ideal for use in all pre-hospital, pre-surgical and resource limited settings.

The role of epigenetics in cardiovascular health and ageing: A focus on physical activity and nutrition.

The cardiovascular system is responsible for transport of blood and nutrients to tissues, and is pivotal to the physiological health and longevity. Epigenetic modification is a natural, age-associated process resulting in highly contextualised gene expression with clear implications for cell differentiation and disease onset. Biological/epigenetic age is independent of chronological age, constituting a highly reflective snapshot of an individual's overall health. Accelerated vascular ageing is of major concern, effectively lowering disease threshold. Age-related chronic illness involves a complex interplay between many biological processes and is modulated by non-modifiable and modifiable risk factors. These alter the static genome by a number of epigenetic mechanisms, which change gene expression in an age and lifestyle dependent manner. This 'epigenetic drift' impacts health and contributes to the etiology of chronic illness. Lifestyle factors may cause acceleration of this epigenetic "clock", pre-disposing individuals to cardiovascular disease. Nutrition and physical activity are modifiable lifestyle choices, synergistically contributing to cardiovascular health. They represent a powerful potential epigenetic intervention point for effective cardiovascular protective and management strategies. Thus, together with traditional risk factors, monitoring the epigenetic signature of ageing may prove beneficial for tailoring lifestyle to fit biology - supporting the increasingly popular concept of "ageing well".

Data on the regulation of moesin and merlin by the urokinase receptor (uPAR): Model explaining distal activation of integrins by uPAR.

The data presented herein are connected to our research article (doi: 10.1016/j.biocel.2017.04.012) [1], in which we investigated the functional connections between the urokinase receptor (uPAR), and the ezrin/radixin/moesin (ERM) proteins, moesin and merlin [1]. Firstly, a model of action is proposed that enlightens how uPAR regulates distal integrins. In addition, data show the effects of expressing wild-type moesin or permanently active T558D mutant of moesin on angiogenesis and morphology of human aortic endothelial cells (HAEC). Additional data compare the effects of urokinase (uPA, the main ligand of uPAR) on the same cells. Lastly, we provide technical data demonstrating the effects of specific siRNA for moesin and merlin on moesin and merlin expression, respectively.

Moesin and merlin regulate urokinase receptor-dependent endothelial cell migration, adhesion and angiogenesis.

The glycosyl-phosphatidyl-inositol (GPI)-anchored urokinase receptor (uPAR) has no intracellular domain, but nevertheless initiates signalling through proximal interactions with other membrane receptors including integrins. The relationships between uPAR and ezrin/radixin/moesin (ERM) proteins, moesin and merlin have never been explored. Moesin and merlin are versatile membrane-actin links and regulators of receptors signalling, respectively. We show that uPAR controls moesin and merlin, which propagate uPAR-initiated signals and modulate integrin functions, thereby regulating uPAR activity. uPAR rapidly de-phosphorylates moesin and phosphorylates merlin inactivating both proteins, and enhancing cell migration and angiogenesis. Moesin behaves as a molecular switch turning either on or off uPAR signalling through cycles of de-activation/activation, or sustained activation, respectively. Furthermore, moesin is at the crossroads of uPAR-initiated outside-in and inside-out signalling promoting integrin-dependent cell adhesion suggesting that uPAR also activates integrins distally through moesin. Knocking down merlin expression enhanced cell migration and adhesion through different regulation of fibronectin- and vitronectin-binding integrins.

Potential Diagnostic and Prognostic Biomarkers of Epigenetic Drift within the Cardiovascular Compartment.

Biomarkers encompass a wide range of different measurable indicators, representing a tangible link to physiological changes occurring within the body. Accessibility, sensitivity, and specificity are significant factors in biomarker suitability. New biomarkers continue to be discovered, and questions over appropriate selection and assessment of their usefulness remain. If traditional markers of inflammation are not sufficiently robust in their specificity, then perhaps alternative means of detection may provide more information. Epigenetic drift (epigenetic modifications as they occur as a direct function with age), and its ancillary elements, including platelets, secreted microvesicles (MVs), and microRNA (miRNA), may hold enormous predictive potential. The majority of epigenetic drift observed in blood is independent of variations in blood cell composition, addressing concerns affecting traditional blood-based biomarker efficacy. MVs are found in plasma and other biological fluids in healthy individuals. Altered MV/miRNA profiles may also be found in individuals with various diseases. Platelets are also highly reflective of physiological and lifestyle changes, making them extremely sensitive biomarkers of human health. Platelets release increased levels of MVs in response to various stimuli and under a plethora of disease states, which demonstrate a functional effect on other cell types.

Did Neoliberalizing West African Forests Produce a New Niche for Ebola?

A recent study introduced a vaccine that controls Ebola Makona, the Zaire ebolavirus variant that has infected 28,000 people in West Africa. We propose that even such successful advances are insufficient for many emergent diseases. We review work hypothesizing that Makona, phenotypically similar to much smaller outbreaks, emerged out of shifts in land use brought about by neoliberal economics. The epidemiological consequences demand a new science that explicitly addresses the foundational processes underlying multispecies health, including the deep-time histories, cultural infrastructure, and global economic geographies driving disease emergence. The approach, for instance, reverses the standard public health practice of segregating emergency responses and the structural context from which outbreaks originate. In Ebola's case, regional neoliberalism may affix the stochastic "friction" of ecological relationships imposed by the forest across populations, which, when above a threshold, keeps the virus from lining up transmission above replacement. Export-led logging, mining, and intensive agriculture may depress such functional noise, permitting novel spillovers larger forces of infection. Mature outbreaks, meanwhile, can continue to circulate even in the face of efficient vaccines. More research on these integral explanations is required, but the narrow albeit welcome success of the vaccine may be used to limit support of such a program.

Spatial characterization of colonies of the flying fox bat, a carrier of Nipah virus in Thailand.

BACKGROUND: A major reservoir of Nipah virus is believed to be the flying fox genus Pteropus, a fruit bat distributed across many of the world's tropical and sub-tropical areas. The emergence of the virus and its zoonotic transmission to livestock and humans have been linked to losses in the bat's habitat. Nipah has been identified in a number of indigenous flying fox populations in Thailand. While no evidence of infection in domestic pigs or people has been found to date, pig farming is an active agricultural sector in Thailand and therefore could be a potential pathway for zoonotic disease transmission from the bat reservoirs. The disease, then, represents a potential zoonotic risk. To characterize the spatial habitat of flying fox populations along Thailand's Central Plain, and to map potential contact zones between flying fox habitats, pig farms and human settlements, we conducted field observation, remote sensing, and ecological niche modeling to characterize flying fox colonies and their ecological neighborhoods. A Potential Surface Analysis was applied to map contact zones among local epizootic actors. RESULTS: Flying fox colonies are found mainly on Thailand's Central Plain, particularly in locations surrounded by bodies of water, vegetation, and safe havens such as Buddhist temples. High-risk areas for Nipah zoonosis in pigs include the agricultural ring around the Bangkok metropolitan region where the density of pig farms is high. CONCLUSIONS: Passive and active surveillance programs should be prioritized around Bangkok, particularly on farms with low biosecurity, close to water, and/or on which orchards are concomitantly grown. Integration of human and animal health surveillance should be pursued in these same areas. Such proactive planning would help conserve flying fox colonies and should help prevent zoonotic transmission of Nipah and other pathogens.

The dawn of Structural One Health: a new science tracking disease emergence along circuits of capital.

The One Health approach integrates health investigations across the tree of life, including, but not limited to, wildlife, livestock, crops, and humans. It redresses an epistemological alienation at the heart of much modern population health, which has long segregated studies by species. Up to this point, however, One Health research has also omitted addressing fundamental structural causes underlying collapsing health ecologies. In this critical review we unpack the relationship between One Health science and its political economy, particularly the conceptual and methodological trajectories by which it fails to incorporate social determinants of epizootic spillover. We also introduce a Structural One Health that addresses the research gap. The new science, open to incorporating developments across the social sciences, addresses foundational processes underlying multispecies health, including the place-specific deep-time histories, cultural infrastructure, and economic geographies driving disease emergence. We introduce an ongoing project on avian influenza to illustrate Structural One Health's scope and ambition. For the first time researchers are quantifying the relationships among transnational circuits of capital, associated shifts in agroecological landscapes, and the genetic evolution and spatial spread of a xenospecific pathogen.

Evolutionary radiation and the spectrum of consciousness.

Evolution is littered with polyphyletic parallelism: many roads lead to functional Romes. We propose consciousness embodies one such example, and represent it here with an equivalence class structure that factors the broad realm of necessary conditions information theoretic realizations of Baars' global workspace model. The construction suggests many different physiological systems can support rapidly shifting, highly tunable, and even simultaneous temporary assemblages of interacting unconscious cognitive modules. The discovery implies various animal taxa exhibiting behaviors we broadly recognize as conscious are, in fact, expressing different forms of the same underlying phenomenon. The variety of possibilities suggests minds today may be only a small surviving fraction of ancient evolutionary radiations--bush phylogenies of consciousness pruned by selection and chance extinction. Although few traces of the radiations may be found in the fossil record, exaptations and vestiges are scattered across the living mind.

Breeding Influenza: The Political Virology of Offshore Farming.

The geographic extent, xenospecificity, and clinical course of influenza A (H5N1), the bird flu strain, suggest the virus is an excellent candidate for a pandemic infection. Much attention has been paid to the virus's virology, pathogenesis and spread. In contrast, little effort has been aimed at identifying influenza's social origins. In this article, I review H5N1's phylogeographic properties, including mechanisms for its evolving virulence. The novel contribution here is the attempt to integrate these with the political economies of agribusiness and global finance. Particular effort is made to explain why H5N1 emerged in southern China in 1997. It appears the region's reservoir of near-human-specific recombinants was subjected to a phase change in opportunity structure brought about by China's newly liberalized economy. Influenza, 200 nm long, seems able to integrate selection pressures imposed by human production across continental distances, an integration any analysis of the virus should assimilate in turn.

On the spectrum of prebiotic chemical systems.

We reexamine Eigen's paradox using the asymptotic limit theorems of information theory. Applying the homology between information source uncertainty and free energy density, under rate distortion constraints, the error catastrophe emerges as the lowest energy state for simple prebiotic systems without error correction. Invoking the usual compartmentalization--i.e., 'vesicles'--and using a Red Queen argument, suggests that information crosstalk between two or more properly interacting structures can initiate a coevolutionary dynamic having at least two quasi-stable states. The first is a low energy realm near the error threshold, and, depending on available energy, the second can approach zero error as a limit. A large deviations argument produces jet-like global transitions which, over sufficient time, may enable shifts between the many quasi-stable modes available to more complicated structures, 'locking in' to some subset of the various possible low error rate chemical systems, which become subject to development by selection and chance extinction. Energy availability, according to the model, is thus a powerful necessary condition for low error rate replication, suggesting that some fundamental prebiotic ecosystem transformation entrained reproductive fidelity. This work, then, supports speculation that our RNA/DNA world may indeed be only the chance result of a very broad prebiotic evolutionary phenomenon. Processes in vitro, or ex planeta, might have other outcomes.

Influenza A H5N1 immigration is filtered out at some international borders.

BACKGROUND: Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space. METHODOLOGY AND PRINCIPAL FINDINGS: We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus. CONCLUSIONS: The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone.

A statistical phylogeography of influenza A H5N1.

The geographic diffusion of highly pathogenic influenza A H5N1 has largely been traced from the perspective of the virus's victims. Birds of a variety of avian orders have been sampled across localities, and their infection has been identified by a general genetic test. Another approach tracks the migration from the perspective of the virus alone, by way of a phylogeography of H5N1 genetic sequences. Although several phylogenies in the literature have labeled H5N1 clades by geographic region, none has analytically inferred the history of the virus's migration. With a statistical phylogeography of 192 hemagglutinin and neuraminidase isolates, we show that the Chinese province of Guangdong is the source of multiple H5N1 strains spreading at both regional and international scales. In contrast, Indochina appears to be a regional sink, at the same time demonstrating bidirectional dispersal among localities within the region. An evolutionary trace of HA(1) across the phylogeography suggests a mechanism by which H5N1 is able to infect repeated cycles of host species across localities, regardless of the host species first infected in each locale. The trace also hypothesizes amino acid replacements that preceded the first recorded outbreak of pathogenic H5N1 in Hong Kong, 1997.

Ugandan Kaposi's sarcoma-associated herpesvirus phylogeny: evidence for cross-ethnic transmission of viral subtypes.

OBJECTIVE: The aim of this study was to test the relationship between Kaposi's sarcoma-associated herpesvirus (KSHV) phylogeny and host ethnicity at the within-country scale. METHODS: KSHV genomic DNA samples were isolated from 31 patients across eleven Ugandan ethnic groups. Amino acid sequences of the ORF-K1 gene were used to construct a neighbor-joining phylogenetic tree. RESULTS: A5 and B1 variants predominated with no evidence of distinct ethnic or geographic distribution. A new K1 subtype (F) was identified in a member of the Bantu Gisu tribe and a new subtype B variant (B3) among members of the Bantu Ganda tribe. CONCLUSIONS: The phylogeny may yet be structured by host ethnicity if members of Ugandan groups have convoluted biological origins, even as they identify with single tribes. An alternative possibility is that KSHV subtype evolution may have preceded major diversification of sub-Saharan Africans into ethnicities as we know them today, with ethnic groups beginning their histories already hosting multiple subtypes. A third alternative is that horizontal transmission of multiple KSHV subtypes may have broken up vertical lineages of the virus passed down within Ugandan populations.

Adaptive chronic infection, structured stress, and medical magic bullets: do reductionist cures select for holistic diseases?

With a generalized language-of-thought argument for immune cognition, we model how population-directed, structured, psychosocial stress can impose an image of itself on the coevolutionary conflict between a highly adaptive chronic infection and the immune response. As population-level structured stress appears a fundamental part of the biology of disease, we raise the possibility that simplistic individual-oriented magic-bullet drug treatments, vaccines, and risk-reduction programs that do not address the fundamental living and working conditions which underlie disease ecology will fail to control many current epidemics. In addition, such reductionist interventions may go so far as to select for more holistic pathogens characterized by processes operating at multiple levels of biocultural organization. The complications are representative of the concerns of cultural immunology, a new field of study.