Beryllium binding at neutral pH: the importance of the Be-O-Be motif

Beryllium speciation at physiological conditions is critical to understanding chronic beryllium disease (CBD). The MHC-class II receptor alleles that have been linked to CBD have more than six carboxylates in a short 20 amino acid segment of the binding pocket and it has been suggested that beryllium may bind within the MHC-class II receptor via the carboxylates. Previous reports also show that citric acid binds beryllium significantly stronger than similar carboxylate ligands such as tartaric acid and is one of the few ligands that can compete with hydrolysis to solubilize beryllium across the entire pH range at molar concentrations. We have characterized the binding of Be to citric acid and shown using a combination of NMR, mass spectrometry and ligand competition studies that Be2L and Be4L2 species dominate. A Be-O-Be linkage with the bridging oxygen coming from the aliphatic alcohol is critical to the stability of the complex. We show through competition experiments that the most stable Be-O-Be arrangement has one Be in a five-member ring and the other Be in a six-member ring. The unusual deprotonation of an aliphatic alcohol (pK(a) = 18) at neutral pH has significant ramifications on the potential interactions of Be with biological ligands such as carbohydrates and Ser and Thr residues.     

Protein and ligand enhanced dissolution of BeO at pH 7

Be is a toxic metal used in both aerospace and defense industries. Lung exposure to Be can lead to a specific immune response called chronic beryllium disease (CBD). CBD has the unique characteristics that it can be triggered by very low level exposures, yet the onset of systems can be delayed from one to over 20 years. This variable delay in the onset of systems implies that a change in the local environment leads to dissolution and bio-availability of the particulate Be. We report here on the dissolution of the highly insoluble BeO in the presence of known Be ligands including the iron transport protein, transferrin, and the ubiquitous citric acid. The presence of ligands even at the 100 μM level led to dissolution of Be to levels that have been shown to cause immune response in both the blood and the lung. Dissolution occurred at pH 7 and was significantly enhanced in a 10 mM phosphate buffer.     

Beryllium Increases the CD14dimCD16+ Subset in the Lung of Chronic Beryllium Disease

CD14^dimCD16+ and CD14^brightCD16+ cells, which compose a minor population of monocytes in human peripheral blood mononuclear cells (PBMC), have been implicated in several inflammatory diseases. The aim of this study was to investigate whether this phenotype was present as a subset of lung infiltrative alveolar macrophages (AMs) in the granulomatous lung disease, chronic beryllium disease (CBD). The monocytes subsets was determined from PBMC cells and bronchoalveolar lavage (BAL) cells from CBD, beryllium sensitized Non-smoker (BeS-NS) and healthy subjects (HS) using flow cytometry. The impact of smoking on the AMs cell phenotype was determined by using BAL cells from BeS smokers (BeS-S). In comparison with the other monocyte subpopulations, CD14^dimCD16+ cells were at decreased frequency in PBMCs of both BeS-NS and CBD and showed higher HLA-DR expression, compared to HS. The AMs from CBD and BeS-NS demonstrated a CD14^dimCD16+phenotype, while CD14^brightCD16+ cells were found at increased frequency in AMs of BeS, compared to HS. Fresh AMs from BeS-NS and CBD demonstrated significantly greater CD16, CD40, CD86 and HLA-DR than HS and BeS-S. The expression of CD16 on AMs from both CBD and BeS-NS was downregulated significantly after 10μM BeSO₄ stimulation. The phagocytic activity of AMs decreased after 10μM BeSO₄ treatment in both BeS-NS and CBD, although was altered or reduced in HS and BeS-S. These results suggest that Be increases the CD14^dimCD16+ subsets in the lung of CBD subjects. We speculate that Be-stimulates the compartmentalization of a more mature CD16+ macrophage phenotype and that in turn these macrophages are a source of Th1 cytokines and chemokines that perpetuate the Be immune response in CBD. The protective effect of cigarette smoking in BeS-S may be due to the low expression of co-stimulatory markers on AMs from smokers as well as the decreased phagocytic function.     

Identification of pathogenic T cells in patients with beryllium-induced lung disease.

Chronic beryllium disease (CBD) is caused by beryllium exposure and is characterized by granulomatous inflammation with accumulation of CD4+ T cells in the lung. We analyzed TCR beta-chain and alpha-chain genes expressed by these CD4+ T cells. In the lungs of individual patients, as well as among four of five CBD patients studied, different oligoclonal expansions within the Vbeta3 subset were found to express homologous or even identical CDR3 amino acid sequences. These related expansions were specific for CBD patients, were compartmentalized to lung, and persisted at high frequency in patients with active disease. Limiting dilution cloning and analysis of coexpressed TCR alpha-chain genes confirmed that these TCRs were selectively expanded by a common Ag involving beryllium. Overall, homologous TCR beta- and alpha-chains showed identical V regions and invariant charged residues within the CDR3 but considerable variability in TCRJ usage. Remarkably, CBD patients expressing nearly identical TCRs did not share common HLA-DRB1 or DQ alleles. These results implicate particular CD4+ cells in the pathogenesis of CBD and provide insight into how beryllium is recognized in human disease.     

Potential binding modes of beryllium with the class II major histocompatibility complex HLA-DP: a combined theoretical and structural database study

In an effort to understand the molecular basis of chronic beryllium disease (CBD), a study of the chemical relationship between beryllium, antigen, and the major histocompatibility complex II, HLA-DP, was undertaken. A homology model of the HLA-DP protein was developed. An analysis of the sequences of HLA-DPB1 and HLA-DPA1 alleles most common among CBD patients revealed several carboxylate rich regions in the peptide-binding cleft. These regions contain many hard Lewis base sites that may provide bonding opportunities for beryllium, a hard Lewis acid. Quantum chemistry calculations and structural database results support the presence of beryllium clusters, bridged by carboxylate, hydroxo, and/or oxo ligands, in the HLA-DP binding cleft. These results strongly suggest that beryllium clusters are an integral part of the antigen, and may even act solely as antigen. This work provides an initial model for thinking about beryllium interactions with proteins relevant to CBD and other metal-induced diseases.     

Beryllium skin patch testing to analyze T cell stimulation and granulomatous inflammation in the lung

Chronic beryllium disease (CBD) is characterized by granulomatous inflammation and the accumulation of CD4(+) T cells in the lung. Patch testing of CBD patients with beryllium sulfate results in granulomatous inflammation in the skin. We investigated whether the T cell clonal populations present in the lung of CBD patients would also be present in the involved skin of a positive beryllium patch test and thus mirror the granulomatous process in the lung. CBD patients with clonal TCR expansions in bronchoalveolar lavage (BAL) were selected for study. All three CBD patients studied had a positive response to beryllium sulfate application and a negative patch test to normal saline. Immunohistochemistry showed extensive infiltration with CD4(+) T cells and few, if any, CD8(+) T cells both at 3 days and at later times when granulomas were apparent. T cell infiltration early after skin testing appeared to be nonspecific with the TCR repertoire of infiltrating T cells being distinct from that present in BAL. At later times when granulomas were present, T cell clones in skin overlapped with those in BAL in all patients tested. Total TCR matches in skin and BAL were as high as 40% in selected Vbeta T cell subsets. Studies of peripheral blood T cells before and after patch testing provided evidence for mobilization of large numbers of pathogenic beryllium-reactive T cells into the circulating pool. These studies using skin patch testing provide new insight into the dynamics of T cell influx and mobilization during granulomatous inflammation.     

Land management: data availability and process understanding for global change studies

In the light of daunting global sustainability challenges such as climate change, biodiversity loss and food security, improving our understanding of the complex dynamics of the Earth system is crucial. However, large knowledge gaps related to the effects of land management persist, in particular those human‐induced changes in terrestrial ecosystems that do not result in land‐cover conversions. Here, we review the current state of knowledge of ten common land management activities for their biogeochemical and biophysical impacts, the level of process understanding and data availability. Our review shows that ca. one‐tenth of the ice‐free land surface is under intense human management, half under medium and one‐fifth under extensive management. Based on our review, we cluster these ten management activities into three groups: (i) management activities for which data sets are available, and for which a good knowledge base exists (cropland harvest and irrigation); (ii) management activities for which sufficient knowledge on biogeochemical and biophysical effects exists but robust global data sets are lacking (forest harvest, tree species selection, grazing and mowing harvest, N fertilization); and (iii) land management practices with severe data gaps concomitant with an unsatisfactory level of process understanding (crop species selection, artificial wetland drainage, tillage and fire management and crop residue management, an element of crop harvest). Although we identify multiple impediments to progress, we conclude that the current status of process understanding and data availability is sufficient to advance with incorporating management in, for example, Earth system or dynamic vegetation models in order to provide a systematic assessment of their role in the Earth system. This review contributes to a strategic prioritization of research efforts across multiple disciplines, including land system research, ecological research and Earth system modelling.     

Getting to the guts of the matter: The status and potential of ‘omics’ research of parasitic protists of the human gastrointestinal system

Parasitic protists are a major cause of diarrhoeal illnesses in humans globally. Collectively, enteric pathogens exceed all other forms of infectious disease, in terms of their estimated global prevalence and socioeconomic impact. They have a disproportionately high impact on children in impoverished communities, leading to acute (diarrhoea, vomiting, dehydration and death) and chronic disease (malabsorption, malnutrition, physical and cognitive stunting and predisposition to chronic, non-communicable disease) consequences. However, historically, investment in research and disease control measures has been disproportionately poor, leading to their current classification as neglected pathogens. A sound understanding of their biology is essential in underpinning detection, treatment and control efforts. One major tool in rapidly improving our knowledge of these parasites is the use of biological systems, including ‘omic’ technologies. In recent years, these tools have shown significant success when applied to enteric protists. This review summarises much of this knowledge and highlights the significant remaining knowledge gaps. A major focus of the present review was to provide a perspective on a way forward to address these gaps using advanced biotechnologies.     

HLA-DP allele-specific T cell responses to beryllium account for DP-associated susceptibility to chronic beryllium disease

Occupational exposure to small molecules, such as metals, is frequently associated with hypersensitivity reactions. Chronic beryllium (Be) disease (CBD) is a multisystem granulomatous disease that primarily affects the lung, and occurs in approximately 3% of individuals exposed to this element. Immunogenetic studies have demonstrated a strong association between CBD and possession of alleles of HLA-DP containing glutamic acid (Glu) at position 69 in the HLA-DP beta-chain. T cell clones were raised from three patients with CBD in whom exposure occurred 10 and 30 years previously. Of 25 Be-specific clones that were obtained, all were restricted by HLA-DP alleles with Glu at DP beta69. Furthermore, the proliferative responses of the clones were absolutely dependent upon DP beta Glu(69) in that a single amino acid substitution at this position abolished the response. As befits a disease whose pathogenesis involves a delayed type hypersensitivity response, the large majority of Be-specific clones secreted IFN-gamma (Th1) and little or no IL-4 (Th2) cytokines. This study provides insights into the molecular basis of DP2-associated susceptibility to CBD.     

Up-regulation of programmed death-1 expression on beryllium-specific CD4+ T cells in chronic beryllium disease

Chronic beryllium disease (CBD) is caused by workplace exposure to beryllium and is characterized by the accumulation of memory CD4+ T cells in the lung. These cells respond vigorously to beryllium salts in culture by producing proinflammatory Th1-type cytokines. The presence of these inflammatory cytokines leads to the recruitment of alveolar macrophages, alveolitis, and subsequent granuloma development. It has been shown that chronic exposure to conventional Ags leads to up-regulation in the expression of negative regulators of T cells such as programmed death-1 (PD-1). Due to the persistence of beryllium in the lung after the cessation of exposure, aberrant regulation of the PD-1 pathway may play an important role in CBD development. In the present study, PD-1 expression was measured on blood and bronchoalveolar lavage (BAL) CD4+ T cells from beryllium-sensitized and CBD subjects. PD-1 expression was significantly higher on BAL CD4+ T cells compared with those cells in blood, with the highest expression on the beryllium-specific T cell subset. In addition, the expression of PD-1 on BAL CD4+ T cells directly correlated with the severity of the T cell alveolitis. Increased expression of the PD-1 ligands, PD-L1 and PD-L2, on BAL CD14+ cells compared with blood was also seen. The addition of anti-PD-1 ligand mAbs augmented beryllium-induced CD4+ T cell proliferation, and an inverse correlation was seen between PD-1 expression on beryllium-specific CD4+ T cells and beryllium-induced proliferation. Thus, the PD-1 pathway is active in beryllium-induced disease and plays a key role in controlling beryllium-induced T cell proliferation.     

The pathogenesis of beryllium-induced pulmonary granulomatosis. A scanning secondary ion analytical microscopy study

Chronic granulomatous pneumonitis was induced in rats with beryllium to study the pathogenesis of that disease, by identifying and localizing the beryllium in histological sections of the pulmonary tissues. This was done with scanning secondary ion mass spectrometry (SIMS). Thus, our observations suggest that the route of the Be from the site of injection into the lung, passes first by the blood, through the vascular wall and into the surrounding pulmonary tissues where Be was phagocytized by macrophages. There resulted in acute vasculitis throughout the lung. It was noted that the granuloma were focal inflammatory sites, solely observed within the vascular wall, distributed along the course of the affected vessel. These findings raise the question as to whether pulmonary granulomatous lesions of other origins are also localized within the vascular wall.     

Recombinant HLA-DP2 binds beryllium and tolerizes beryllium-specific pathogenic CD4+ T cells

Chronic beryllium disease is a lung disorder caused by beryllium exposure in the workplace and is characterized by granulomatous inflammation and the accumulation of beryllium-specific, HLA-DP2-restricted CD4+ T lymphocytes in the lung that proliferate and secrete Th1-type cytokines. To characterize the interaction among HLA-DP2, beryllium, and CD4+ T cells, we constructed rHLA-DP2 and rHLA-DP4 molecules consisting of the alpha-1 and beta-1 domains of the HLA-DP molecules genetically linked into single polypeptide chains. Peptide binding to rHLA-DP2 and rHLA-DP4 was consistent with previously published peptide-binding motifs for these MHC class II molecules, with peptide binding dominated by aromatic residues in the P1 pocket. 9Be nuclear magnetic resonance spectroscopy showed that beryllium binds to the HLA-DP2-derived molecule, with no binding to the HLA-DP4 molecule that differs from DP2 by four amino acid residues. Using beryllium-specific CD4+ T cell lines derived from the lungs of chronic beryllium disease patients, beryllium presentation to those cells was independent of Ag processing because fixed APCs were capable of presenting BeSO4 and inducing T cell proliferation. Exposure of beryllium-specific CD4+ T cells to BeSO4 -pulsed, plate-bound rHLA-DP2 molecules induced IFN-gamma secretion. In addition, pretreatment of beryllium-specific CD4+ T cells with BeSO4-pulsed, plate-bound HLA-DP2 blocked proliferation and IL-2 secretion upon re-exposure to beryllium presented by APCs. Thus, the rHLA-DP2 molecules described herein provide a template for engineering variants that retain the ability to tolerize pathogenic CD4+ T cells, but do so in the absence of the beryllium Ag.     

Coping with Drought: Towards a Multilevel Understanding Based on Conservation of Resources Theory

There is substantial research on psychological consequences of disasters. However, most disaster studies to date have focused on acute disasters, ignoring slow-onset chronic hazards, such as extreme climate conditions and pollution. Using a multilevel theoretical framework based on the Conservation of Resources theory (S. E. Hobfoll, The Ecology of Stress, Hemisphere, New York, 1988; Stress, Culture, and Community: The Psychology and Philosophy of Stress, Plenum, New York, 1998) and the “ecological analogy” (see e.g., S. E. Hobfoll and R. S Lilly, Journal of Community Psychology, 21:128–148, 1993; E. J. Trickett, Extreme Stress and Communities: Impact and Intervention, Kluwer, Boston, 1995), this critical review of the current literature is aimed at increasing our understanding of personal and community impacts of drought as a classic example of a natural, slow-onset disaster affecting large numbers of people worldwide. A gap in the current literature was identified concerning appraisal and coping at the individual level. These include psychological coping strategies and the role of resources other than economic resources in explaining vulnerability to negative consequences of drought, such as personal resources (e.g., knowledge, skills, self-sufficiency, mastery, control) and social resources (e.g., social support). Important differences were identified with fast-onset disasters. Most importantly, dealing with drought is generally an integrated part of life for people in drought prone areas. Therefore, individuals may not recognize that their problems are part of a community wide stressor, and raising community awareness during severe and long droughts that deplete community resources needs special attention. Implications for studying drought and effective intervention strategies are given.     

Beryllium presentation to CD4+ T cells is dependent on a single amino acid residue of the MHC class II beta-chain

Chronic beryllium disease (CBD) is characterized by a CD4+ T cell alveolitis and granulomatous inflammation in the lung. Genetic susceptibility to this disease has been linked with HLA-DP alleles, particularly those possessing a glutamic acid at position 69 (Glu69) of the beta-chain. However, 15% of CBD patients do not possess a Glu69-containing HLA-DP allele, suggesting that other MHC class II alleles may be involved in disease susceptibility. In CBD patients without a Glu69-containing HLA-DP allele, an increased frequency of HLA-DR13 alleles has been described, and these alleles possess a glutamic acid at position 71 of the beta-chain (which corresponds to position 69 of HLA-DP). Thus, we hypothesized that beryllium presentation to CD4+ T cells was dependent on a glutamic acid residue at the identical position of both HLA-DP and -DR. The results show that HLA-DP Glu69- and HLA-DR Glu71-expressing molecules are capable of inducing beryllium-specific proliferation and IFN-gamma expression by lung CD4+ T cells. Using fibroblasts expressing mutated HLA-DP2 and -DR13 molecules, beryllium recognition was dependent on the glutamic acid at position 69 of HLA-DP and 71 of HLA-DR, suggesting a critical role for this amino acid in beryllium presentation to Ag-specific CD4+ T cells. Thus, these results demonstrate that a single amino acid residue of the MHC class II beta-chain dictates beryllium presentation and potentially, disease susceptibility.     

Beryllium uptake by excised barley roots

The uptake of beryllium by excised barley roots from a solutioncontaining 111 µM beryllium and 500 µM calcium wasstudied. The exchange-adsorbed portion was 15% of the totalBe uptake after 30 min of exposure. The total Be content couldbe reduced to 55% of the control in 1 hr with demineralizedwater. At pH levels above 6, Be uptake was increased dramatically.A Q₁₀ of 1.2 was found to exist between 1 and 23°C. Mg (111µM) did not influence Be absorption while Zn and Al atthe same concentration reduced it, possibly competitively, 27and 62% of the control, respectively. Dinitro-phenol (500 µM),cyanide (500µM), azide (500 µM) and m-chlorocarbonylcyanidephenylhydrazone (100 µM) at least doubled it indicatingthe existence of a possible metabolic barrier to beryllium entrywhich was disrupted by these compounds. Absorption kineticsover an external beryllium concentration range of 11 to 444µM suggested a number of binding sites. Above 444 µMa scattering effect was noted due possibly to its toxic effect. ¹Pesticide Programs, Environmental Protection Agency (P.S. -769),Washington, D.C. 20460, U.S.A. (Received August 13, 1979; )     

The biomechanical integrin

The integrin lies at the center of our efforts to understand mechanotransduction in the human body. Over the past two decades, a wealth of information has yielded important insights into integrin structure and functioning in biochemical pathways; however, relatively little emphasis has been placed on mechanics. In this article, we review the current knowledge base of integrin mechanobiology by examining the role of integrins in stabilizing tissue structure, the mechanisms of integrin force transfer, the process of cell migration, and the pathology of cancer. In order to successfully address the gaps in cancer and other disease research going forward, future efforts of integrin mechanobiology must focus on examining cells in 3D environments and integrating our current understanding into computational models that predict the behavior of integrins in non-equilibrium interactions.     

Electrophysiological recording from parasitic nematode muscle

Infection of man and animals with parasitic nematodes is recognized as a significant global problem (McLeod in Int J Parasitol 25(11):1363–1367, 1994; Hotez et al. in N Engl J Med 357(10):1018–1027, 2007). At present control of these infections relies primarily on chemotherapy. There are a limited number of classes of anthelmintic compounds and the majority of these act on ion-channels of the parasite (Martin et al. in Parasitology 113:S137–S156, 1996). In this report, we describe electrophysiological recording techniques as applied to parasitic nematodes. The aim of this report is: (1) to promote the study of ion channels in nematodes to help further the understanding of antinematodal drug action; (2) to describe our recording equipment and experimental protocols; and (3) provide some examples of the information to be gleaned from this approach and how it can increase our understanding of these important pathogens.     

Progress in mining the human proteome for disease applications

Currently available technologies allow in-depth analysis of multiple facets of the proteome that have clinical relevance and that complement current genomics-based approaches. Although some progress has been made in our knowledge of the human proteome in health and in disease, there is an urgent need to chart a coherent road map with clearly defined milestones to guide proteomics efforts. Areas of emphasis include: (1) building resources, (2) filling gaps in our understanding of biological variation, and (3) systematically characterizing proteome alterations that occur in well-defined disease states, all of which require an organized and collaborative effort.     

Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2

Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within the acidic pocket (Glu26, Glu68 and Glu69) present on the HLA-DP2 protein in accordance with the experimental work [1]. In addition, the modeling indicates that the Be ion binds to the HLA-DP2 before the corresponding peptide is able to bind to it. Further analysis of the MD generated trajectories reveals that in the presence of the Be ion in the binding pocket of HLA-DP2, all the different types of peptides induce very similar conformational changes, but their binding affinities are quite different. Since these conformational changes are distinctly different from the changes caused by peptides normally found in the cell in the absence of Be, it can be speculated that CBD can be caused by any peptide in presence of Be ion. However, the affinities of peptides for Be loaded HLA-DP2 were found to depend of their amino acid composition and the peptides carrying acidic group at positions 4 and 7 are among the strongest binders. Thus, it is proposed that CBD is caused by the exposure of Be of an individual carrying the HLA-DP2*0201 allele and that the binding of Be to HLA-DP2 protein alters the conformational and ionization properties of HLA-DP2 such that the binding of a peptide triggers a wrong signaling cascade.     

Building a 2010 biodiversity conservation data baseline: contributions of the Group on Earth Observations

Characterizing, modeling, and monitoring the distribution and condition of the Earth’s biodiversity and ecosystems has a long history of being aided by Earth Observation data and the models and derivative products that they support. At the global scale, there need to be more coordinated efforts to acquire, process, analyze, and make available these observation data across all disciplines, particularly since many applications use the same primary and derived data. Towards that end, the Group on Earth Observations (GEO) is implementing the Global Earth Observing System of Systems. The purpose of this article is to provide information on GEO’s goals and activities relevant to biodiversity and ecosystems. The article also describes the data that would best serve as a year 2010 baseline in order to support the objectives of the Convention on Biological Diversity (CBD) as well as many other international agreements, programs, and activities. Indeed, an assessment of existing biodiversity observations with a concomitant recognition of the remaining gaps will promote the establishment of an integrated framework for biodiversity observations in support of the CBD’s efforts.