Improving the integrity and reproducibility of research that uses antibodies: a technical, data sharing, behavioral and policy challenge.

Antibodies are one of the most important reagents used in biomedical and fundamental research, used to identify, and quantify proteins, contribute to knowledge of disease mechanisms, and validate drug targets. Yet many antibodies used in research do not recognize their intended target, or recognize additional molecules, compromising the integrity of research findings and leading to waste of resources, lack of reproducibility, failure of research projects, and delays in drug development. Researchers frequently use antibodies without confirming that they perform as intended in their application of interest. Here we argue that the determinants of end-user antibody choice and use are critical, and under-addressed, behavioral drivers of this problem. This interacts with the batch-to-batch variability of these biological reagents, and the paucity of available characterization data for most antibodies, making it more difficult for researchers to choose high quality reagents and perform necessary validation experiments. The open-science company YCharOS works with major antibody manufacturers and knockout cell line producers to characterize antibodies, identifying high-performing renewable antibodies for many targets in neuroscience. This shows the progress that can be made by stakeholders working together. However, their work so far applies to only a tiny fraction of available antibodies. Where characterization data exists, end-users need help to find and use it appropriately. While progress has been made in the context of technical solutions and antibody characterization, we argue that initiatives to make best practice behaviors by researchers more feasible, easy, and rewarding are needed. Global cooperation and coordination between multiple partners and stakeholders will be crucial to address the technical, policy, behavioral, and open data sharing challenges. We offer potential solutions by describing our Only Good Antibodies initiative, a community of researchers and partner organizations working toward the necessary change. We conclude with an open invitation for stakeholders, including researchers, to join our cause.

Dryness of ephemeral lakes and consequences for dust activity: the case of the Hamoun drainage basin, southeastern Iran.

This study examines the influence of changes in the water coverage in the Hamoun dry-bed lakes on visibility, dust outbreaks, aerosol loading and land-atmospheric fluxes over the region covering the period 1985-2005. The Hamoun basin, located on the southeastern Iran and western Afghanistan borders, has been recognized as one of the major dust source regions in south Asia and is covered by shallow, marshy lakes that are fed by the Helmand and Farahrood rivers. When the water in watersheds that support the lakes is drawn down for natural or human-induced reasons, the end result is a decrease in the water coverage in the basin, or even complete dryness as occurred in 2001. Then, strong seasonal winds, mainly in summer, blow fine sand and silt off the exposed lakebed, enhancing dust activity and aerosol loading over the region. Satellite (Landsat) and meteorological observations reveal that the water levels in the Hamoun lakes exhibit considerable inter-annual variability during the period 1985-2005 strongly related to anomalies in precipitation. This is the trigger for concurrent changes in the frequency of the dusty days, aerosol loading and deterioration of visibility over the region, as satellite (TOMS, MODIS, MISR) observations reveal. On the other hand, soil moisture and latent heat, obtained via model (GLDAS_noah-10) simulations are directly linked with water levels and precipitation over the region. The desiccation of the Hamoun lakes in certain years and the consequent increase in frequency and intensity of dust storms are serious concerns for the regional climate, ecosystems and human health.

The method of surface PEGylation influences leukocyte adhesion and activation.

The influence of different surface modifications with poly(ethyleneglycol) (PEG) layers on the adsorption of fibrinogen and the adhesion and activation of macrophage-like human leukocytes was investigated. Poly(ethylene terephthalate) (PET) was modified using pulsed AC plasma polymerization with two types of starting monomers to generate: 1) a reactive acid surface using maleic anhydride (MAH) as monomer, and 2) a PEG-like surface using diethyleneglycol methyl vinyl ether (DEGVE) as monomer. The MAH surface was used as a reactive platform to graft linear chains of non-fouling mPEG via an intermediate layer of poly(ethyleneimine) (PEI) under lower critical solution temperature (LCST) conditions of the mPEG. The DEGVE monomer is used to create PEG-like layers by use of low power plasma conditions. The ability of the surfaces to resist protein adsorption was investigated quantitatively using (125)I-radiolabeled human fibrinogen, and the conformation of the adsorbed protein was tested using an anti-fibrinogen monoclonal antibody in an enzyme-linked immunosorbent assay. The results showed that PEGylated surfaces adsorbed significantly less (up to 90% less) fibrinogen, and that unfolding of adsorbed fibrinogen was more pronounced on the linear mPEG layers than on the PEG-like plasma polymer surfaces. Adhesion of in-vitro differentiated macrophage-like U937 cells was reduced on both the PEG-like plasma polymer surfaces and the linear mPEG layers compared to the unmodified PET surface, but cells adhering to the PEG-like plasma polymer surfaces secreted less tumor necrosis factor-alpha (TNF-alpha) than cells adhering to the linear mPEG layers. In conclusion, the method for preparing non-fouling surfaces for long-term implanted devices influence surface-induced cellular responses of the host.

Arf family GTPases: roles in membrane traffic and microtubule dynamics.

Database mining and phylogenetic analysis of the Arf (ADP-ribosylation factor) superfamily revealed the presence in mammals of at least 22 members, including the six Arfs, two Sars and 14 Arl (Arf-like) proteins. At least six Arf family members were found in very early eukaryotes, including orthologues of Arf, Sar, Arl2, Arl3, Arl6 and Arl8. While roles for Arfs in membrane traffic are well known, those for most of the Arls remain unknown. Depletion in cells of the most closely related human Arf proteins, Arf1-Arf5, reveals specificities among their cellular roles and suggests that they may function in pairs at different steps in endocytic and secretory membrane traffic. In addition, recent results from a number of laboratories suggest that several of the Arl proteins may be involved in different aspects of microtubule-dependent functions. Thus, a second major role for Arf family GTPases, that of regulating microtubules, is emerging. Because membrane traffic is often dependent upon movement of vesicles along microtubules this raises the possibility that these two fundamental functions of Arf family members, regulation of vesicle traffic and microtubule dynamics, diverged from one function of Arfs in the earliest cells that has continued to branch and allow additional levels of regulation.

Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases.

Structures were determined by x-ray crystallography for two members of the ADP-ribosylation factor (ARF) family of regulatory GTPases, yeast ARF1 and ARL1, and were compared with previously determined structures of human ARF1 and ARF6. These analyses revealed an overall conserved fold but differences in primary sequence and length, particularly in an N-terminal loop, lead to differences in nucleotide and divalent metal binding. Packing of hydrophobic residues is central to the interplay between the N-terminal alpha-helix, switch I, and the interswitch region, which along with differences in surface electrostatics provide explanations for the different biophysical and biochemical properties of ARF and ARF-like proteins.

A conservative amino acid substitution alters the regiospecificity of CYP94A2, a fatty acid hydroxylase from the plant Vicia sativa.

Fatty acid omega-hydroxylation is involved in the biosynthesis of the plant cuticle, formation of plant defense signaling molecules, and possibly in the rapid catabolism of free fatty acids liberated under stress conditions. CYP94A2 is a cytochrome P450-dependent medium-chain fatty acid hydroxylase that was recently isolated from Vicia sativa. Contrary to CYP94A1 and CYP86A1, two other fatty acid hydroxylases previously characterized in V. sativa and Arabidopsis thaliana, CYP94A2 is not a strict omega-hydroxylase, but exhibits chain-length-dependent regioselectivity of oxidative attack. Sequence alignments of CYP94A2 with CYP94A1 and molecular modeling studies suggested that F494, located in SRS-6 (substrate recognition site) was involved in substrate recognition and positioning. Indeed, a conservative amino acid substitution at that position markedly altered the regiospecificity of CYP94A2. The observed shift from omega toward omega-1 hydroxylation was prominent with lauric acid as substrate and declined with increasing fatty acid chain length.

Activation of the luteinizing hormone/choriogonadotropin hormone receptor promotes ADP ribosylation factor 6 activation in porcine ovarian follicular membranes.

Previously we demonstrated in a cell-free ovarian follicular plasma membrane model that agonist-dependent desensitization of the luteinizing hormone/choriogonadotropin receptor (LH/CG R) is GTP-dependent, mimicked by the addition of ADP-ribosylation factor (ARF) nucleotide binding site opener, which acts as a guanine nucleotide exchange factor for ARFs 1 and 6, and selectively inhibited by synthetic N-terminal ARF6 peptides. We therefore sought direct evidence that activation of the LH/CG R promotes activation of ARF1 and/or ARF6. Using a classic ARF activation assay, the cholera toxin-catalyzed ADP-ribosylation of G alpha(s), results show that LH/CG R activation stimulates an ARF protein by a brefeldin A-independent mechanism. Synthetic N-terminal inhibitory ARF6 but not ARF1 peptide blocks LH/CG R-stimulated ARF activity. LH/CG R activation also promotes the binding of a photoaffinity GTP analog to a protein that migrates on one- and two-dimensional polyacrylamide gel electrophoresis with ARF6. These results suggest that ARF6 is the predominant ARF activated by the LH/CG R. To activate ARF6, the LH/CG R does not appear to signal through the C-terminal regions of G alpha(i) or G alpha(q) or through the second or third intracellular loops or the N terminus of the cytoplasmic tail of the LH/CG R. Although exogenous recombinant ARNO promotes only a small increase in ARF6 activation in the presence of activated LH/CG R, hCG-stimulated ARF6 activation is reduced to basal levels by catalytically inactive ARF nucleotide binding-site opener. These results provide direct evidence that LH/CG R activation leads to the activation of membrane-delimited ARF6.

Plant sterol 14 alpha-demethylase affinity for azole fungicides.

Azole fungicides were thought to have much greater affinity for the fungal cytochrome P450 enzyme, sterol 14 alpha-demthylase (CYP51) than the plant orthologue. Using purified CYP51 from the plant Sorghum bicolor L Moenech, a direct comparison of the sensitivity to the fungicides triadimenol and tebuconazole has been carried out. S. bicolor CYP51 was purified to homogenity as determined by SDS--PAGE and specific heme content. Addition of the azole fungicides triadimenol and tebuconazole induced type II spectral changes, with saturation occurring at equimolar azole/P450 concentrations. Inhibition of reconstituted activities revealed only a threefold insensitivity of the plant CYP51 compared to a fungal CYP51, from the phytopathogen Ustilago maydis, as judged by IC(50) values. The implications for fungicide mode of action and application are discussed.

The Escherichia coli heat labile toxin binds to Golgi membranes and alters Golgi and cell morphologies using ADP-ribosylation factor-dependent processes.

The fate of the catalytic subunit of the Escherichia coli heat labile toxin (LTA(1)) was studied after expression in mammalian cells to assess the requirement for ADP-ribosylation factor (ARF) binding to localization and toxicity and ability to compete with endogenous ARF effectors. A progression in LTA(1) localization from cytosol to binding Golgi stacks to condensation of Golgi membranes was found to correlate with the time and level of LTA(1) expression. At the highest levels of LTA(1) expression the staining of LTA and both extrinsic and lumenal Golgi markers all became diffuse, in a fashion reminiscent of the actions of brefeldin A. Thus, LTA(1) binds to the Golgi and can alter its morphology in two distinct ways. However, point mutants of LTA(1) that are defective in the ability to bind activated ARF were also unable to bind Golgi membranes or modify Golgi morphology. Co-expression of mutants of ARF3 that regained binding to these same mutant LTA(1) proteins restored the localization and activities of the toxin. Thus, binding to ARF is required both for the localization of the toxin to the Golgi and for effects on Golgi membranes. A correlation was also seen between the ability of LTA mutants to bind ARF and the increase in cellular cAMP levels. These results demonstrate the importance of ARF binding to the toxicity and cellular effects of the ADP-ribosylating bacterial toxin and reveal that mutants defective in binding ARF retain basal ADP-ribosylation activity but are the least toxic LTA(1) mutants yet described, making them the best candidates for development as mucosal adjuvants.

ARF binds the C-terminal region of the Escherichia coli heat-labile toxin (LTA1) and competes for the binding of LTA2.

Cholera toxin (CT) and the heat-labile enterotoxin (LT) from Escherichia coli are highly related in terms of structure and biochemical activities and are the causative agents of cholera and traveler's diarrhea, respectively. The pathophysiological action of these toxins requires their activity as ADP-ribosyltransferases, transferring the ADP-ribose moiety from NAD onto the stimulatory, regulatory component of adenylyl cyclase, Gs. This reaction is highly dependent on the protein cofactor, termed ADP-ribosylation factor (ARF), that is itself a 20 kDa regulatory GTPase. In this study, we define sites of interaction between LTA and human ARF3. The residues identified as important to ARF binding include several of those previously shown to bind to the A2 subunit of the toxin and those important to the organization of two flexible loops, previously implicated as regulators of substrate entry. A model for how ARF acts to enhance the catalytic activity is proposed. A critical portion of the overlap between ARF and LTA(2) in binding LTA(1) includes a short region of sequence homology between LTA(2) and the switch II region of ARF. LTA(2) also interacted with ARF effectors in two-hybrid assays, and thus, we discuss the possibility that the LTA(2) subunit may function in cells as a partial ARF mimetic to compete for the binding of ARF to LTA(1) or regulate aspects of the toxin's transport from the cell surface to the ER.

ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1-binding proteins.

Despite the 40-60% identity between ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins, distinct functional roles have been inferred from findings that ARLs lack the biochemical or genetic activities characteristic of ARFs. The potential for functional overlap between ARFs and ARLs was examined by comparing effects of expression on intact cells and the ability to bind effectors. Expression of [Q71L]ARL1 in mammalian cells led to altered Golgi structure similar to, but less dramatic than, that reported previously for [Q71L]ARF1. Two previously identified partners of ARFs, MKLP1 and Arfaptin2/POR1, also bind ARL1 but not ARL2 or ARL3. Two-hybrid screens of human cDNA libraries with dominant active mutants of human ARL1, ARL2, and ARL3 identified eight different but overlapping sets of binding partners. Specific interactions between ARL1 and two binding proteins, SCOCO and Golgin-245, are defined and characterized in more detail. Like ARFs and ARL1, the binding of SCOCO to Golgi membranes is rapidly reversed by brefeldin A, suggesting the presence of a brefeldin A-sensitive ARL1 exchange factor. These data reveal a complex network of interactions between GTPases in the ARF family and their effectors and reveal a potential for cross-talk not demonstrated previously.

Safety and efficacy of high-dose adenosine-induced asystole during endovascular AAA repair.

PURPOSE: To assess the safety and efficacy of high-dose adenosine administration to increase the precision of endovascular abdominal aortic aneurysm (AAA) repair using a balloon deployed stent-graft. METHODS: From January 1997 to March 1999, 98 AAA patients (79 men; mean age 71 years, range 62-91) were treated with balloon-expandable stent-grafts under an approved protocol. After placing a temporary transvenous ventricular lead or an external transthoracic pacing electrode, adenosine (24 mg initially) was administered in an escalating dose fashion to induce at least 10 seconds of asystole, during which the proximal stent was expanded. RESULTS: Adenosine dosages ranged from 24 to 90 mg (median 24 mg). Nine (9.2%) self-limiting cardiac events were observed: 2 (2.0%) episodes of transient myocardial ischemia, 2 (2.0%) cases of atrial fibrillation requiring cardioversion, 1 (1.0%) transient left bundle branch block lasting <10 seconds, and 4 (4.1%) prolonged periods of asystole requiring temporary pacemaker activation. There were no cases of bronchospasm or worsening obstructive pulmonary disease, and no patients required inotropic support after adenosine-induced asystole. CONCLUSIONS: Cardiac events following adenosine-induced asystole are infrequent, mild, and easily treated. The perioperative use of high-dose adenosine to ensure precise stent-graft placement appears to be a safe method of inducing temporary asystole during endovascular aortic repair.

Effectors increase the affinity of ADP-ribosylation factor for GTP to increase binding.

The stoichiometry of the binding of GTP to ADP-ribosylation factor (ARF) proteins, normally quite low at approximately 0.05 mol/mol protein, was found to increase to a maximum of 1 mol/mol in the presence of effectors. The mechanism of this action was found to result from the ability of these effectors to increase the affinity of ARF for activating guanine nucleotide triphosphates. The existence of a conformation of ARF with low affinity (>100 micrometer) for GTP is proposed. The actions of effectors to increase the equilibrium binding of GTP is interpreted as evidence that these same effectors interact with and modulate the affinity of the inactive ARF for GTP. A new model for these interactions among ARF, effectors, and GTP is proposed, and a preliminary test in cells is supportive of these observations with relevance to signaling in cells.

The ADP ribosylation factor nucleotide exchange factor ARNO promotes beta-arrestin release necessary for luteinizing hormone/choriogonadotropin receptor desensitization.

Desensitization of guanine nucleotide binding protein-coupled receptors is a ubiquitous phenomenon characterized by declining effector activity upon persistent agonist stimulation. The luteinizing hormone/choriogonadotropin receptor (LH/CGR) in ovarian follicles exhibits desensitization of effector adenylyl cyclase activity in response to the mid-cycle surge of LH. We have previously shown that uncoupling of the agonist-activated LH/CGR from the stimulatory G protein (G(s)) is dependent on GTP and attributable to binding of beta-arrestin present in adenylyl cyclase-rich follicular membrane fraction to the third intracellular (3i) loop of the receptor. Here, we report that LH/CGR-dependent desensitization is mimicked by ADP ribosylation factor nucleotide-binding site opener, a guanine nucleotide exchange factor of the small G proteins ADP ribosylation factors (Arfs) 1 and 6, and blocked by synthetic N-terminal Arf6 peptide, suggesting that the GTP-dependent step of LH/CGR desensitization is receptor-dependent Arf6 activation. Arf activation by GTP and ADP ribosylation factor nucelotide-binding site opener promotes the release of docked beta-arrestin from the membrane, making beta-arrestin available for LH/CGR; Arf6 but not Arf1 peptides block beta-arrestin release from the membrane. Thus, LH/CGR appears to activate two membrane delimited signaling cascades via two types of G proteins: heterotrimeric G(s) and small G protein Arf6. Arf6 activation releases docked beta-arrestin necessary for receptor desensitization, providing a feedback mechanism for receptor self-regulation.

A family of ADP-ribosylation factor effectors that can alter membrane transport through the trans-Golgi.

A family of three structurally related proteins were cloned from human cDNA libraries by their ability to interact preferentially with the activated form of human ADP-ribosylation factor 3 (ARF3) in two-hybrid assays. The specific and GTP-dependent binding was later confirmed through direct protein binding of recombinant proteins. The three proteins share large ( approximately 300 residues) domains at their N termini that are 60-70% identical to each other and a shorter (73 residues) domain at their C termini with 70% homology to the C-terminal "ear" domain of gamma-adaptin. Although GGA1 is found predominantly as a soluble protein by cell fractionation, all three proteins were found to localize to the trans-Golgi network (TGN) by indirect immunofluorescence. The binding of GGAs to TGN was sensitive to brefeldin A, consistent with this being an ARF-dependent event. Thus, these proteins have been named Golgi-localizing, gamma-adaptin ear homology domain, ARF-binding proteins, or GGAs. The finding that overexpression of GGAs was sufficient to alter the distribution of markers of the TGN (TGN38 and mannose 6-phosphate receptors) led us to propose that GGAs are effectors for ARFs that function in the regulation of membrane traffic through the TGN.

Effects of activated ADP-ribosylation factors on Golgi morphology require neither activation of phospholipase D1 nor recruitment of coatomer.

Nine mutations in the switch I and switch II regions of human ADP-ribosylation factor 3 (ARF3) were isolated from loss-of-interaction screens, using two-hybrid assays with three different effectors. We then analyzed the ability of the recombinant proteins to (i) bind guanine nucleotides, (ii) activate phospholipase D1 (PLD1), (iii) recruit coatomer (COP-I) to Golgi-enriched membranes, and (iv) expand and vesiculate Golgi in intact cells. Correlations of activities in these assays were used as a means of testing specific hypotheses of ARF action, including the role of PLD1 activation in COP-I recruitment, the role of COP-I in Golgi vesiculation caused by expression of the dominant activating mutant [Q71L]ARF3, and the need for PLD1 activation in Golgi vesiculation. Because we were able to find at least one example of a protein that has lost each of these activities with retention of the others, we conclude that activation of PLD1, recruitment of COP-I to Golgi, and vesiculation of Golgi in cells are functionally separable processes. The ability of certain mutants of ARF3 to alter Golgi morphology without changes in PLD1 activity or COP-I binding is interpreted as evidence for at least one additional, currently unidentified, effector for ARF action at the Golgi.

Residues forming a hydrophobic pocket in ARF3 are determinants of GDP dissociation and effector interactions.

Three residues of human ADP-ribosylation factor 3 (ARF3) (F51, W66 and Y81) cluster into a hydrophobic pocket in the inactive, GDP-bound protein. Disruption of the hydrophobic pocket with mutations at these residues increased the rate of GDP dissociation and association, but not always that of GTPgammaS. Several of the same mutants were found to be defective, often selectively, in binding different ARF effectors in two-hybrid assays. These results highlight three features of these hydrophobic residues in regulating (1) the rate of GDP dissociation, (2) the conformational changes that promote GTP binding and (3) their role in binding target proteins.

Arf proteins bind to mitotic kinesin-like protein 1 (MKLP1) in a GTP-dependent fashion.

Arf proteins comprise a family of 21-kDa GTP-binding proteins with many proposed functions in mammalian cells, including the regulation of several steps of membrane transport, maintenance of organelle integrity, and activation of phospholipase D. We performed a yeast two-hybrid screen of human cDNA libraries using a dominant activating allele, [Q71L], of human Arf3 as bait. Eleven independent isolates contained plasmids encoding the C-terminal tail of mitotic kinesin-like protein-1 (MKLP1). Further deletion mapping allowed the identification of an 88 amino acid Arf3 binding domain in the C-terminus of MKLP1. This domain has no clear homology to other Arf binding proteins or to other proteins in the protein databases. The C-terminal domain of MKLP1 was expressed and purified from bacteria as a GST fusion protein and shown to bind Arf3 in a GTP-dependent fashion. A screen for mutations in Arf3 that specifically lost the ability to bind MKLP1 identified 10 of 14 point mutations in the GTP-sensitive switch I or switch II regions of Arf3. Two-hybrid assays of the C-terminal domain of MKLP1 with each of the human Arf isoforms revealed strong interaction with each. Taken together, these data are all supportive of the conclusion that activated Arf proteins bind to the C-terminal "tail" domain of MKLP1.

Adenosine-induced transient asystole for management of a basilar artery aneurysm. Case report.

Advances in anesthetic and surgical management, such as induced deep hypothermic circulatory arrest and application of temporary clips, have improved outcome for patients with basilar artery aneurysms. Nonetheless, these techniques are associated with significant risks. The authors report a case in which three transient periods of cardiac asystole were induced during basilar artery aneurysm surgery. Adenosine-induced asystole facilitated the safe clipping of the aneurysm by producing consistent periods of profound hypotension and collapse of the aneurysm without the need for temporary clipping. This technique provided unencumbered identification of perforating arteries, precise definition of the local anatomy, and an ideal environment for the safe placement of the aneurysm clip.

Intraoperative rupture of an abdominal aortic aneurysm during an endovascular stent-graft procedure.

PURPOSE: To highlight the risk of intraoperative rupture as a complication of endovascular aortic repair. CLINICAL FEATURES: An 81-yr-old man was admitted for endovascular aortic repair of a 6 cm infrarenal abdominal aortic aneurysm. After establishment of a conduction blockade using a combined spinal-epidural technique, a balloon-activated endovascular stent-graft was advanced to the proximal aneurysmal neck. Approximately four minutes after the stent-graft was deployed, the mean arterial pressure decreased to 30 mmHg and the heart rate increased to 135 bpm. While fluid and vasoactive medications were administered and the airway was secured, repeat aortography confirmed contrast extravasation into the retroperitoneal space at the junction of the proximal aortic neck and the aneurysm sac. The angioplasty deployment balloon was repositioned and inflated proximal to the presumed site of aortic rupture, thus providing aortic control until an open repair of the aorta was undertaken. CONCLUSION: Although endovascular stent-graft placement may be a less invasive method than conventional open aortic reconstruction, it must be recognized that the potential for devastating consequences such as aortic rupture is present.