Extracellular ionic locks determine variation in constitutive activity and ligand potency between species orthologs of the free fatty acid receptors FFA2 and FFA3

Free fatty acid receptors 2 and 3 (FFA2 and FFA3) are G protein-coupled receptors for short chain free fatty acids (SCFAs). They respond to the same set of endogenous ligands but with distinct rank-order of potency, such that acetate (C2) has been described as FFA2 selective while propionate (C3) is non-selective. Although C2 was confirmed to be selective for human FFA2 over FFA3, this ligand was not selective between the mouse orthologs. Moreover, although C3 was indeed not selective between the human orthologs it displayed clear selectivity for mouse FFA3 over mouse FFA2. This altered selectivity to C2 and C3 resulted from broad differences in SCFAs potency at the mouse orthologs. In studies to define the molecular basis for these observations marked variation in ligand-independent, constitutive activity was identified. The orthologs with higher potency for the SCFAs, human FFA2 and mouse FFA3, displayed high constitutive activity while the orthologs with lower potency for the agonist ligands, mouse FFA2 and human FFA3, did not. Sequence alignments of the 2nd extracellular loop identified single negatively charged residues in FFA2 and FFA3 not conserved between species and predicted to form ionic lock interactions with arginine residues within the FFA2 or FFA3 agonist binding pocket to regulate constitutive activity and SCFA potency. Reciprocal mutation of these residues between species orthologs resulted in the induction (or repression) of constitutive activity, and in most cases also yielded corresponding changes in SCFA potency.

Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen Fasciola hepatica:Expansion of a repertoire of virulence-associated factors

Cathepsin L proteases secreted by the helminth pathogen Fasciola hepatica have functions in parasite virulence including tissue invasion and suppression of host immune responses. Using proteomics methods alongside phylogenetic studies we characterized the profile of cathepsin L proteases secreted by adult F. hepatica and hence identified those involved in host-pathogen interaction. Phylogenetic analyses showed that the Fasciola cathepsin L gene family expanded by a series of gene duplications followed by divergence that gave rise to three clades associated with mature adult worms (Clades 1, 2, and 5) and two clades specific to infective juvenile stages (Clades 3 and 4). Consistent with these observations our proteomics studies identified representatives from Clades 1, 2, and 5 but not from Clades 3 and 4 in adult F. hepatica secretory products. Clades 1 and 2 account for 67.39 and 27.63% of total secreted cathepsin Ls, respectively, suggesting that their expansion was positively driven and that these proteases are most critical for parasite survival and adaptation. Sequence comparison studies revealed that the expansion of cathepsin Ls by gene duplication was followed by residue changes in the S2 pocket of the active site. Our biochemical studies showed that these changes result in alterations in substrate binding and suggested that the divergence of the cathepsin L family produced a repertoire of enzymes with overlapping and complementary substrate specificities that could cleave host macromolecules more efficiently. Although the cathepsin Ls are produced as zymogens containing a prosegment and mature domain, all secreted enzymes identified by MS were processed to mature active enzymes. The prosegment region was highly conserved between the clades except at the boundary of prosegment and mature enzyme. Despite the lack of conservation at this section, sites for exogenous cleavage by asparaginyl endopeptidases and a Leu-Ser[downward arrow]His motif for autocatalytic cleavage by cathepsin Ls were preserved.

Structural and functional relationships in the virulence-associated cathepsin L proteases of the parasitic liver fluke, Fasciola hepatica

The helminth parasite Fasciola hepatica secretes cysteine proteases to facilitate tissue invasion, migration, and development within the mammalian host. The major proteases cathepsin L1 (FheCL1) and cathepsin L2 (FheCL2) were recombinantly produced and biochemically characterized. By using site-directed mutagenesis, we show that residues at position 67 and 205, which lie within the S2 pocket of the active site, are critical in determining the substrate and inhibitor specificity. FheCL1 exhibits a broader specificity and a higher substrate turnover rate compared with FheCL2. However, FheCL2 can efficiently cleave substrates with a Pro in the P2 position and degrade collagen within the triple helices at physiological pH, an activity that among cysteine proteases has only been reported for human cathepsin K. The 1.4-A three-dimensional structure of the FheCL1 was determined by x-ray crystallography, and the three-dimensional structure of FheCL2 was constructed via homology-based modeling. Analysis and comparison of these structures and our biochemical data with those of human cathepsins L and K provided an interpretation of the substrate-recognition mechanisms of these major parasite proteases. Furthermore, our studies suggest that a configuration involving residue 67 and the "gatekeeper" residues 157 and 158 situated at the entrance of the active site pocket create a topology that endows FheCL2 with its unusual collagenolytic activity. The emergence of a specialized collagenolytic function in Fasciola likely contributes to the success of this tissue-invasive parasite.

Density Functional study of the photoactive yellow protein's chromophore

We have investigated the structural and electronic properties of p-coumaric acid, the chromophore of the photoactive yellow protein (PYP), by means of first-principles molecular dynamics based on density functional theory (DFT). We have studied the chromophore both in the vacuum and in an extended model which includes the nearest residues in the binding pocket of PYP, as derived from crystallographic data. We have characterized the ground state of the isolated chromophore in its protonated and deprotonated forms and computed the energy barrier involved in the trans to cis isomerization process around the carbon-carbon double bond. A comparison of the optimized structures of the chromophore in the vacuum and in the extended protein model, both in the trans (ground state of PYP in the dark) and cis (first light-activated intermediate) configuration, shows how the protein environment affects the chromophore in the first step of the photocycle. Our model gives an energy storage of 25 kcal/mol associated with the trans-to-cia photoisomerization. Finally, we have elucidated the nature of the electronic excitation relevant for the photochemistry of PYP by means of time-dependent DFT calculations.

Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses one of the two steps in glycolysis which generate the reduced coenzyme NADH. This reaction precedes the two ATP generating steps. Thus, inhibition of GAPDH will lead to substantially reduced energy generation. Consequently, there has been considerable interest in developing GAPDH inhibitors as anti-cancer and anti-parasitic agents. Here, we describe the biochemical characterisation of GAPDH from the common liver fluke Fasciola hepatica (FhGAPDH). The primary sequence of FhGAPDH is similar to that from other trematodes and the predicted structure shows high similarity to those from other animals including the mammalian hosts. FhGAPDH lacks a binding pocket which has been exploited in the design of novel antitrypanosomal compounds. The protein can be expressed in, and purified from Escherichia coli; the recombinant protein was active and showed no cooperativity towards glyceraldehyde 3-phosphate as a substrate. In the absence of ligands, FhGAPDH was a mixture of homodimers and tetramers, as judged by protein-protein crosslinking and analytical gel filtration. The addition of either NAD(+) or glyceraldehyde 3-phosphate shifted this equilibrium towards a compact dimer. Thermal scanning fluorimetry demonstrated that this form was considerably more stable than the unliganded one. These responses to ligand binding differ from those seen in mammalian enzymes. These differences could be exploited in the discovery of reagents which selectively disrupt the function of FhGAPDH.

Skin-reducing mastectomy and one-stage implant reconstruction with a myodermal flap: A safe and effective technique in risk-reducing and therapeutic mastectomy

Introduction: Immediate reconstruction following mastectomy for breast cancer has been shown to be oncologically safe and associated with improved psychosocial outcomes for patients. Bostwick described a technique for one-stage implant based reconstruction, combining skin-sparing mastectomy with concurrent reduction of the skin envelope. This report reviews the experience of a single centre using skin-reducing mastectomy and one-stage implant reconstruction in both early stage breast cancer and risk-reducing mastectomy, with specific reference to frequency of complications, implant loss and oncological outcomes.

Methods and results: A retrospective review was undertaken to identify women who had undergone skin-reducing mastectomy and one-stage implant reconstruction using a de-epithelialised dermal flap, between October 2008 and October 2012. One hundred and four consecutive mastectomies, with reconstruction, were performed by two surgeons on 64 patients. No complications were seen in 43.8% of patients. At three months, four implants were lost (3.8% of breast reconstructions, 6.3% of patients), due to either peri-implant infection or mastectomy skin flap necrosis. One patient required unplanned return to theatre for evacuation of a haematoma. Minor mastectomy skin flap necrosis was seen in 10 breasts (9.6% of reconstructed breasts) and superficial wound infection in 8 breasts (7.7% of reconstructed breasts). All of these complications were managed conservatively and none required operative intervention. At a median follow up of 35 months (4-53 months) there had been one episode of ipsilateral axillary nodal recurrence.

Conclusion: One-stage implant reconstruction using a myo-dermal flap technique following skin-reducing mastectomy is safe and should be considered in selected patients. Most complications are minor and will resolve with conservative management. Major complications such as implant failure or immediate reoperation, were relatively uncommon (6.3% patients, 3.8% of reconstructed breasts). Early follow-up suggests that oncological outcomes are satisfactory, but longer follow-up is required to substantiate this. (C) 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

A statistical characterization of shadowed device-to-device communications in an indoor environment

This paper presents the results of a measurement campaign aimed at characterizing and modeling the indoor radio channel between two hypothetical cellular handsets. The device-to-device channel measurements were made at 868 MHz and investigated a number of different everyday scenarios such as the devices being held at the user's heads, placed in a pocket and one of the devices placed on a desktop. The recently proposed shadowed k-μ fading model was used to characterize these channels and was shown to provide a good description of the measured data. It was also evident from the experiments, that the device-to-device communications channel is susceptible to shadowing caused by the human body.

Channel measurements of device–to–device communications in an urban outdoor environment

In this paper, the results of radio channel measurements between two hypothetical cellular handsets in an outdoor urban environment are reported. The device-to-device channel measurements were made at 868 MHz and investigated a number of different everyday usage scenarios such as the devices being held at the user's heads, placed in a pocket while one of the users rotated or both moved randomly. It was found that shadowing of the main signal path caused by the human body will be an important factor in future device-to-device communications at this frequency. The recently proposed shadowed κ-μ fading model was used to characterize these channels and shown to provide a good description of the measured data.

P3 SAR exploration of biphenyl carbamate based Legumain inhibitors

This Letter describes the further development and SAR exploration of a novel series of Legumain inhibitors. Based upon a previously identified Legumain inhibitor from our group, we explored the SAR of the carbamate phenyl ring system to probe the P3 pocket of the enzyme. This led to the identification of a sub-nanomolar inhibitor of Legumain.



Graphical abstract

The rise of the digital citizen-stakeholder: rebalancing multistakeholder governance

The principle feature in the evolution of the internet has been its ever growing reach to include old and young, rich and poor. The internet’s ever encroaching presence has transported it from our desktop to our pocket and into our glasses. This is illustrated in the Internet Society Questionnaire on Multistakeholder Governance, which found the main factors affecting change in the Internet governance landscape were more users online from more countries and the influence of the internet over daily life. The omnipresence of the internet is self- perpetuating; its usefulness grows with every new user and every new piece of data uploaded. The advent of social media and the creation of a virtual presence for each of us, even when we are not physically present or ‘logged on’, means we are fast approaching the point where we are all connected, to everyone else, all the time. We have moved far beyond the point where governments can claim to represent our views which evolve constantly rather than being measured in electoral cycles.
The shift, which has seen citizens as creators of content rather than consumers of it, has undermined the centralist view of democracy and created an environment of wiki democracy or crowd sourced democracy. This is at the heart of what is generally known as Web 2.0, and widely considered to be a positive, democratising force. However, we argue, there are worrying elements here too. Government does not always deliver on the promise of the networked society as it involves citizens and others in the process of government. Also a number of key internet companies have emerged as powerful intermediaries harnessing the efforts of the many, and re- using and re-selling the products and data of content providers in the Web 2.0 environment. A discourse about openness and transparency has been offered as a democratising rationale but much of this masks an uneven relationship where the value of online activity flows not to the creators of content but to those who own the channels of communication and the metadata that they produce.
In this context the state is just one stakeholder in the mix of influencers and opinion formers impacting on our behaviours, and indeed our ideas of what is public. The question of what it means to create or own something, and how all these new relationships to be ordered and governed are subject to fundamental change. While government can often appear slow, unwieldy and even irrelevant in much of this context, there remains a need for some sort of political control to deal with the challenges that technology creates but cannot by itself control. In order for the internet to continue to evolve successfully both technically and socially it is critical that the multistakeholder nature of internet governance be understood and acknowledged, and perhaps to an extent, re- balanced. Stakeholders can no longer be classified in the broad headings of government, private sector and civil society, and their roles seen as some sort of benign and open co-production. Each user of the internet has a stake in its efficacy and each by their presence and participation is contributing to the experience, positive or negative of other users as well as to the commercial success or otherwise of various online service providers. However stakeholders have neither an equal role nor an equal share. The unequal relationship between the providers of content and those who simple package up and transmit that content - while harvesting the valuable data thus produced - needs to be addressed. Arguably this suggests a role for government that involves it moving beyond simply celebrating and facilitating the on- going technological revolution. This paper reviews the shifting landscape of stakeholders and their contribution to the efficacy of the internet. It will look to critically evaluate the primacy of the individual as the key stakeholder and their supposed developing empowerment within the ever growing sea of data. It also looks at the role of individuals in wider governance roles. Governments in a number of jurisdictions have sought to engage, consult or empower citizens through technology but in general these attempts have had little appeal. Citizens have been too busy engaging, consulting and empowering each other to pay much attention to what their governments are up to. George Orwell’s view of the future has not come to pass; in fact the internet has insured the opposite scenario has come to pass. There is no big brother but we are all looking over each other’s shoulder all the time, while at the same time a number of big corporations are capturing and selling all this collective endeavour back to us.

Kaempferol Exhibits Progestogenic Effects in Ovariectomized Rats

OBJECTIVE: Progesterone (P4) plays a central role in women's health. Synthetic progestins are used clinically in hormone replacement therapy (HRT), oral contraceptives, and for the treatment of endometriosis and infertility. Unfortunately, synthetic progestins are associated with side effects, including cardiovascular disease and breast cancer. Botanical dietary supplements are widely consumed for the alleviation of a variety of gynecological issues, but very few studies have characterized natural compounds in terms of their ability to bind to and activate progesterone receptors (PR). Kaempferol is a flavonoid that functions as a non-steroidal selective progesterone receptor modulator (SPRM) in vitro. This study investigated the molecular and physiological effects of kaempferol in the ovariectomized rat uteri.

METHODS: Since genistein is a phytoestrogen that was previously demonstrated to increase uterine weight and proliferation, the ability of kaempferol to block genistein action in the uterus was investigated. Analyses of proliferation, steroid receptor expression, and induction of well-established PR-regulated targets Areg and Hand2 were completed using histological analysis and qPCR gene induction experiments. In addition, kaempferol in silico binding analysis was completed for PR. The activation of estrogen and androgen receptor signalling was determined in vitro.

RESULTS: Molecular docking analysis confirmed that kaempferol adopts poses that are consistent with occupying the ligand-binding pocket of PRA. Kaempferol induced expression of PR regulated transcriptional targets in the ovariectomized rat uteri, including Hand2 and Areg. Consistent with progesterone-l ke activity, kaempferol attenuated genistein-induced uterine luminal epithelial proliferation without increasing uterine weight. Kaempferol signalled without down regulating PR expression in vitro and in vivo and without activating estrogen and androgen receptors.

CONCLUSION: Taken together, these data suggest that kaempferol is a unique natural PR modulator that activates PR signaling in vitro and in vivo without triggering PR degradation.

Channel Measurements of Device-to-Device Communications at 2.45 GHz

In the future, device-to-device communications will become a fundamental part of cellular communications. Interoperability between handsets will be facilitated using frequencies located in a number of bands including those found in the Industrial, Scientific and Medical (ISM) band at 2.45 GHz. In this paper, we present the results of channel measurements made between two hypothetical cellular handsets operating at 2.45 GHz in an outdoor environment. We consider a range of typical usage scenarios such as both user equipment being held at the head while imitating a voice call, placed in user's pocket for both stationary and dynamic links. A range of parameter estimates obtained using the shadowed κ-μ fading model are also presented.

Neuropeptide Y in GCF in periodontal health and disease

Objectives: To determine whether neuropeptide Y (NPY) is present in gingival crevicular fluid (GCF) in both periodontal health and disease and to study the relationship of NPY with periodontal inflammation. Methods: GCF samples (30 s) were collected from one site with both pocket depth (>4mm) and loss of periodontal attachment (>4mm) in 20 patients with chronic periodontitis (mean age 41.4, SD 9.6 yrs; 10 m, 10 f). GCF was also collected from clinically healthy sites (< 3mm, no bleeding on probing) in 20 subjects with no periodontitis (mean age 37.4, SD 11.7; 10 m, 10 f). GCF was collected using the periopaper strip method, diluted in 500 ul of phosphate-buffered saline and stored at –70°C. Samples were analysed in duplicate for NPY by radioimmunoassay. NPY levels were compared using the Mann-Whitney test. Results: Measurable NPY was present in all the GCF samples collected from healthy subjects. NPY was below the level of detection in 4 (20%) of the diseased subjects. There was considerable variability in the amount of NPY collected from both groups. There were no differences between the levels of NPY measured in males compared with females in either the healthy or diseased groups. Significantly more (P< 0.0001) NPY (pg) was collected from healthy subjects (Median 165, IQR 80; mean 161, SD 64) than diseased subjects (Median 37.5, IQR 56.3; mean 39.8, SD 35.1). There was more variability in the NPY concentration (pg/ul) which was also significantly higher in healthy (Median 575.7, IQR 562.3; mean 645.7, SD 416.7) compared with diseased subjects (Median 43.6, IQR 117.4; mean 96.4, SD 124.5). Conclusions: It is concluded that the levels of NPY in GCF sampled

Using the fluorescent properties of STO-609 as a tool to assist structure-function analyses of recombinant CaMKK2

Calcium/calmodulin-dependent kinase kinase 2 (CaMKK2) has been implicated in the regulation of metabolic activity in cancer and immune cells, and affects whole-body metabolism by regulating ghrelin-signalling in the hypothalamus. This has led to efforts to develop specific CaMKK2 inhibitors, and STO-609 is the standardly used CaMKK2 inhibitor to date. We have developed a novel fluorescence-based assay by exploiting the intrinsic fluorescence properties of STO-609. Here, we report an in vitro binding constant of KD ∼17 nM between STO-609 and purified CaMKK2 or CaMKK2:Calmodulin complex. Whereas high concentrations of ATP were able to displace STO-609 from the kinase, GTP was unable to achieve this confirming the specificity of this association. Recent structural studies on the kinase domain of CaMKK2 had implicated a number of amino acids involved in the binding of STO-609. Our fluorescent assay enabled us to confirm that Phe(267) is critically important for this association since mutation of this residue to a glycine abolished the binding of STO-609. An ATP replacement assay, as well as the mutation of the 'gatekeeper' amino acid Phe(267)Gly, confirmed the specificity of the assay and once more confirmed the strong binding of STO-609 to the kinase. In further characterising the purified kinase and kinase-calmodulin complex we identified a number of phosphorylation sites some of which corroborated previously reported CaMKK2 phosphorylation and some of which, particularly in the activation segment, were novel phosphorylation events. In conclusion, the intrinsic fluorescent properties of STO-609 provide a great opportunity to utilise this drug to label the ATP-binding pocket and probe the impact of mutations and other regulatory modifications and interactions on the pocket. It is however clear that the number of phosphorylation sites on CaMKK2 will pose a challenge in studying the impact of phosphorylation on the pocket unless the field can develop approaches to control the spectrum of modifications that occur during recombinant protein expression in E. coli.