Transcriptional tools: Small molecules for modulating CBP KIX-dependent transcriptional activators

Previously it was demonstrated that amphipathic isoxazolidines are able to functionally replace the transcriptional activation domains of endogenous transcriptional activators. In addition, in vitro binding studies suggested that a key binding partner of these molecules is the CREB Binding Protein (CBP), more specifically the KIX domain within this protein. Here we show that CBP plays an essential role in the ability of isoxazolidine transcriptional activation domains to activate transcription in cells. Consistent with this model, isoxazolidines are able to function as competitive inhibitors of the activators MLL and Jun, both of which utilize a binding interaction with KIX to up-regulate transcription. Further, modification of the N2 side chain produced three analogs with enhanced potency against Jun-mediated transcription, although increased cytotoxicity was also observed. Collectively these small KIX-binding molecules will be useful tools for dissecting the role of the KIX domain in a variety of pathological processes. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 17–23, 2011.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78234/1/21548_ftp.pd

A Synthetic Loop Replacement Peptide That Blocks Canonical NFâ κB Signaling

Aberrant canonical NFâ κB signaling is implicated in diseases from autoimmune disorders to cancer. A major therapeutic challenge is the need for selective inhibition of the canonical pathway without impacting the many nonâ canonical NFâ κB functions. Here we show that a selective peptideâ based inhibitor of canonical NFâ κB signaling, in which a hydrogen bond in the NBD peptide is synthetically replaced by a nonâ labile bond, shows an about 10â fold increased potency relative to the original inhibitor. Not only is this molecule, NBD2, a powerful tool for dissection of canonical NFâ κB signaling in disease models and healthy tissues, the success of the synthetic loop replacement suggests that the general strategy could be useful for discovering modulators of the many proteinâ protein interactions mediated by such structures.A peptideâ based inhibitor of canonical NFâ κB signaling, in which a hydrogen bond in the NBD peptide is synthetically replaced by a nonâ labile bond, shows an about 10â fold increased potency relative to the original inhibitor. The success of the synthetic replacement of a peptide loop suggests that the general strategy could be broadly useful for discovering modulators of many proteinâ protein interactions mediated by such structures.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135096/1/anie201607990.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135096/2/anie201607990-sup-0001-misc_information.pd

Concern level assessment: building domain knowledge into a visual system to support network-security situation awareness

Information officers and network administrators require tools to help them achieve situation awareness about potential network threats. We describe a response to mini-challenge 1 of the 2012 IEEE VAST challenge in which we developed a visual analytic solution to a network security situation awareness problem. To support conceptual design, we conducted a series of knowledge elicitation sessions with domain experts. These provided an understanding of the information they needed to make situation awareness judgements as well as a characterisation of those judgements in the form of production rules which define a parameter we called the ‘Concern Level Assessment’ (CLA). The CLA was used to provide heuristic guidance within a visual analytic system called MSIEVE. An analysis of VAST challenge assessment sessions using M-SIEVE provides some evidence that intelligent heuristics like this can provide useful guidance without unduly dominating interaction and understanding

M-Sieve: a visualisation tool for supporting network security analysts

The Middlesex Spatial Interactive Visualisation Environment (M-Sieve) is a spatiotemporal visual analytics tool for exploring computer network activity. M-Sieve allows the user to filter and visualize data through facets to explore and find patterns. To help guide exploration, we developed a set of rules which are used to derive a variable we call the ‘Concern Level Assessment’ (CLA). The CLA is based on attributes of nodes on the network. The rules were developed by eliciting inferences from network security domain experts. The combination of M-Sieve and the CLA allowed us to address the problem presented by the VAST 2012 Competition - Mini Challenge 1

Exploring efficient seamless handover in VANET systems using network dwell time

Vehicular ad hoc networks are a long-term solution contributing significantly towards intelligent transport systems (ITS) in providing access to critical life-safety applications and services. Although vehicular ad hoc networks are attracting greater commercial interest, current research has not adequately captured the real-world constraints in vehicular ad hoc network handover techniques. Therefore, in order to have the best practice for vehicular ad hoc network services, it is necessary to have seamless connectivity for optimal coverage and ideal channel utilisation. Due to the high velocity of vehicles and smaller coverage distances, there are serious challenges in providing seamless handover from one roadside unit (RSU) to another. Though other research efforts have looked at many issues in vehicular ad hoc networks (VANETs), very few research work have looked at handover issues. Most literature assume that handover does not take a significant time and does not affect the overall VANET operation. In our previous work, we started to investigate these issues. This journal provides a more comprehensive analysis involving the beacon frequency, the size of beacon and the velocity of the vehicle. We used some of the concepts of Y-Comm architecture such as network dwell time (NDT), time before handover (TBH) and exit time (ET) to provide a framework to investigate handover issues. Further simulation studies were used to investigate the relation between beaconing, velocity and the network dwell time. Our results show that there is a need to understand the cumulative effect of beaconing in addition to the probability of successful reception as well as how these probability distributions are affected by the velocity of the vehicle. This provides more insight into how to support life critical applications using proactive handover techniques

Roles for a Lipid Phosphatase in the Activation of its Opposing Lipid Kinase

Fig4 is a phosphoinositide phosphatase that converts PI3,5P2 to PI3P. Paradoxically, mutation of Fig4 results in lower PI3,5P2, indicating that Fig4 is also required for PI3,5P2 production. Fig4 promotes elevation of PI3,5P2, in part, through stabilization of a protein complex that includes its opposing lipid kinase, Fab1, and the scaffold protein Vac14. Here we show that multiple regions of Fig4 contribute to its roles in the elevation of PI3,5P2: Its catalytic site, an N-terminal disease-related surface, and a C-terminal region. We show that mutation of the Fig4 catalytic site enhances the formation of the Fab1-Vac14-Fig4 complex, and reduces the ability to elevate PI3,5P2. This suggests that independent of its lipid phosphatase function, the active site plays a role in the Fab1-Vac14-Fig4 complex. We also show that the N-terminal disease-related surface contributes to the elevation of PI3,5P2 and promotes Fig4 association with Vac14 in a manner that requires the Fig4 C-terminus. We find that the Fig4 C-terminus alone interacts with Vac14 in vivo and retains some functions of full-length Fig4. Thus, a subset of Fig4 functions are independent of its phosphatase domain and at least three regions of Fig4 play roles in the function of the Fab1-Vac14-Fig4 complex

Impact of water hardness on oxytetracycline oral bioavailability in fed and fasted piglets

Water hardness is a critical factor that affects oxytetracycline dissolution by chelation with cations. These interactions may lead to impaired dosing and consequently decrease absorption. Moreover, feed present in gastrointestinal tract may interact with antibiotic and alter pharmacokinetic parameters. In the present study, dissolution profiles of an oxytetracycline veterinary formulation were assessed in purified, soft and hard water. Furthermore, oxytetracycline absolute bioavailability, after oral administration of the drug dissolved in soft or hard water, was evaluated in fed and fasted piglets. A maximum dissolution of 86% and 80% was obtained in soft and hard water, respectively, while in purified water dissolution was complete. Results from in vivo study reconfirmed oxytetracycline´s very low oral bioavailability. The greatest values were attained when antibiotic was dissolved in soft water and in fasted animals. Statistically significant lower absolute bioavailability was achieved when hard water was used and/or animals were fed. Moreover, Cmax attained in all treatments was lower than MIC90 of most important swine pathogens. For these reasons, the oral use of OTC formulations, that have demonstrated low oral bioavailability, should be avoided to treat systemic diseases in pigs.Fil: Decundo, Julieta María. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencia Veterinarias. Departamento de Fisiopatología. Laboratorio de Toxicología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Dieguez, Susana Nelly. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencia Veterinarias. Departamento de Fisiopatología. Laboratorio de Toxicología; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Martínez, Guadalupe. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento de Fisiopatología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Romanelli, Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento de Fisiopatología; ArgentinaFil: Fernández Paggi, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento de Fisiopatología; ArgentinaFil: Pérez, Denisa Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento de Fisiopatología; ArgentinaFil: Amanto, Fabian A.. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento de Producción Animal; ArgentinaFil: Soraci, Alejandro Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencia Veterinarias. Departamento de Fisiopatología. Laboratorio de Toxicología; Argentin

"Engaging with birth stories in pregnancy: a hermeneutic phenomenological study of women's experiences across two generations"

BACKGROUND: The birth story has been widely understood as a crucial source of knowledge about childbirth. What has not been reported is the effect that birth stories may have on primigravid women's understandings of birth. Findings are presented from a qualitative study exploring how two generations of women came to understand birth in the milieu of other's stories. The prior assumption was that birth stories must surely have a positive or negative influence on listeners, steering them towards either medical or midwifery-led models of care. METHODS: A Heideggerian hermeneutic phenomenological approach was used. Twenty UK participants were purposively selected and interviewed. Findings from the initial sample of 10 women who were pregnant in 2012 indicated that virtual media was a primary source of birth stories. This led to recruitment of a second sample of 10 women who gave birth in the 1970s-1980s, to determine whether they were more able to translate information into knowledge via stories told through personal contact and not through virtual technologies RESULTS: Findings revealed the experience of 'being-in-the-world' of birth and of stories in that world. From a Heideggerian perspective, the birth story was constructed through 'idle talk' (the taken for granted assumptions of things, which come into being through language). Both oral stories and those told through technology were described as the 'modern birth story'. The first theme 'Stories are difficult like that', examines the birth story as problematic and considers how stories shape meaning. The second 'It's a generational thing', considers how women from two generations came to understand what their experience might be. The third 'Birth in the twilight of certainty,' examines women's experience of Being in a system of birth as constructed, portrayed and sustained in the stories being shared. CONCLUSIONS: The women pregnant in 2012 framed their expectations in the language of choice, whilst the women who birthed in the 1970s-1980s framed their experience in the language of safety. For both, however, the world of birth was the same; saturated with, and only legitimised by the birth of a healthy baby. Rather than creating meaningful understanding, the 'idle talk' of birth made both cohorts fearful of leaving the relative comfort of the 'system', and of claiming an alternative birth

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein “interactome” includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of special interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.National Institutes of Health (U.S.) (NIH Award GM067681)National Institutes of Health (U.S.) (NCRR Award RR-15301