The Cys-loop pentameric ligand-gated ion channel receptors: 50 years on

This year, 2011, the Department of Pharmacology at the University of Alberta celebrated its 50th anniversary. This timeframe covers nearly the entire history of Cys-loop pentameric ligand-gated ion channel (pLGIC) research. In this review we consider how major technological advancements affected our current understanding of pLGICs, and highlight the contributions made by members of our department. The individual at the center of our story is Susan Dunn; her passing earlier this year has robbed the Department of Pharmacology and the research community of a most insightful colleague. Her dissection of ligand interactions with the nAChR, together with their interpretation, was the hallmark of her extensive collaborations with Michael Raftery. Here, we highlight some electrophysiological studies from her laboratory over the last few years, using the technique that she introduced to the department in Edmonton, the 2-electrode voltage-clamp of Xenopus oocytes. Finally, we discuss some single-channel studies of the anionic GlyR and GABA(A)R that prefaced the introduction of this technique to her laboratory.     

Approach-bias predicts development of cannabis problem severity in heavy cannabis users: results from a prospective FMRI study

A potentially powerful predictor for the course of drug (ab)use is the approach-bias, that is, the pre-reflective tendency to approach rather than avoid drug-related stimuli. Here we investigated the neural underpinnings of cannabis approach and avoidance tendencies. By elucidating the predictive power of neural approach-bias activations for future cannabis use and problem severity, we aimed at identifying new intervention targets. Using functional Magnetic Resonance Imaging (fMRI), neural approach-bias activations were measured with a Stimulus Response Compatibility task (SRC) and compared between 33 heavy cannabis users and 36 matched controls. In addition, associations were examined between approach-bias activations and cannabis use and problem severity at baseline and at six-month follow-up. Approach-bias activations did not differ between heavy cannabis users and controls. However, within the group of heavy cannabis users, a positive relation was observed between total lifetime cannabis use and approach-bias activations in various fronto-limbic areas. Moreover, approach-bias activations in the dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC) independently predicted cannabis problem severity after six months over and beyond session-induced subjective measures of craving. Higher DLPFC/ACC activity during cannabis approach trials, but lower activity during cannabis avoidance trials were associated with decreases in cannabis problem severity. These findings suggest that cannabis users with deficient control over cannabis action tendencies are more likely to develop cannabis related problems. Moreover, the balance between cannabis approach and avoidance responses in the DLPFC and ACC may help identify individuals at-risk for cannabis use disorders and may be new targets for prevention and treatment.     

Self-organizing ontology of biochemically relevant small molecules

Background  

The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.     

Process attributes in bio-ontologies

ABSTRACT: BACKGROUND: Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency. RESULTS: We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity. CONCLUSIONS: We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity.     

Intestinal aspartate proteases TiCatD and TiCatD2 of the haematophagous bug Triatoma infestans (Reduviidae): sequence characterisation, expression pattern and characterisation of proteolytic activity

Two aspartate protease encoding complementary deoxyribonucleic acids (cDNA) were characterised from the small intestine (posterior midgut) of Triatoma infestans and the corresponding genes were named TiCatD and TiCatD2. The deduced 390 and 393 amino acid sequences of both enzymes contain two regions characteristic for cathepsin D proteases and the conserved catalytic aspartate residues forming the catalytic dyad, but only TiCatD2 possesses an entire C-terminal proline loop. The amino acid sequences of TiCatD and TiCatD2 show 51-58% similarity to other insect cathepsin D-like proteases and, respectively, 88 and 58% similarity to the aspartate protease ASP25 from T. infestans available in the GenBank database. In phylogenetic analysis, TiCatD and ASP25 clearly separate from cathepsin D-like sequences of other insects, TiCatD2 groups with cathepsin D-like proteases with proline loop. The activity of purified TiCatD and TiCatD2 was highest between pH 2 and 4, respectively, and hence, deviate from the pH values of the lumen of the small intestine, which varied in correlation with the time after feeding between pH 5.2 and 6.7 as determined by means of micro pH electrodes. Both cathepsins, TiCatD and TiCatD2, were purified from the lumen of the small intestine using pepstatin affinity chromatography and identified by nanoLC-ESI-MS/MS analysis as those encoded by the cDNAs. The proteolytic activity of the purified enzymes is highest at pH 3 and the respective genes are expressed in the both regions of the midgut, stomach (anterior midgut) and small intestine, not in the rectum, salivary glands, Malpighian tubules or haemocytes. The temporal expression pattern of both genes in the small intestine after feeding revealed a feeding dependent regulation for TiCatD but not for TiCatD2.     

Mutation of the PDK1 PH domain inhibits protein kinase B/Akt, leading to small size and insulin resistance

PDK1 activates a group of kinases, including protein kinase B (PKB)/Akt, p70 ribosomal S6 kinase (S6K), and serum and glucocorticoid-induced protein kinase (SGK), that mediate many of the effects of insulin as well as other agonists. PDK1 interacts with phosphoinositides through a pleckstrin homology (PH) domain. To study the role of this interaction, we generated knock-in mice expressing a mutant of PDK1 incapable of binding phosphoinositides. The knock-in mice are significantly small, insulin resistant, and hyperinsulinemic. Activation of PKB is markedly reduced in knock-in mice as a result of lower phosphorylation of PKB at Thr308, the residue phosphorylated by PDK1. This results in the inhibition of the downstream mTOR complex 1 and S6K1 signaling pathways. In contrast, activation of SGK1 or p90 ribosomal S6 kinase or stimulation of S6K1 induced by feeding is unaffected by the PDK1 PH domain mutation. These observations establish the importance of the PDK1-phosphoinositide interaction in enabling PKB to be efficiently activated with an animal model. Our findings reveal how reduced activation of PKB isoforms impinges on downstream signaling pathways, causing diminution of size as well as insulin resistance.     

Rift Valley fever knowledge,mitigation strategies and communication preferences among male and female livestock farmers in Eastern Province,Rwanda

The Government of Rwanda reported an outbreak of Rift Valley fever (RVF) in the Eastern Province in 2018. To respond to the outbreak, vaccination and education campaigns about the disease were carried out. Because RVF cases continue to be detected in Rwanda and the disease impacts livelihoods and health, accurate knowledge and communication are imperative. The objectives of this study were to evaluate knowledge and risk perceptions of RVF transmission among livestock farmers in Nyagatare District, Eastern Province, Rwanda, and to compare RVF knowledge, risk perceptions, and farming practices between male and female livestock farmers. This cross-sectional, quantitative study was conducted in selected sectors of Nyagatare District in the Eastern Province of Rwanda in June 2019. A 34-question survey was used to ask about demographics, livestock ownership, risk perceptions about zoonotic diseases and livestock management, RVF knowledge, preferred communication sources and information sharing strategies, and protective strategies for RVF mitigation while working with livestock. Livestock farmers were interviewed at three milk collection centers, two village meeting points, a farm cooperative meeting, and during door-to-door visits in villages. In total, 123 livestock farmers were interviewed. The survey found that most livestock farmers lacked knowledge about epizootic and zoonotic transmission of RVF, more male livestock farmers were familiar with RVF and risk mitigation strategies, and female livestock farmers are not viewed as reliable sources of information. Additionally, most livestock farmers had not vaccinated their animals against RVF despite past vaccination campaigns. Radio was the most popular communication channel. These findings show that RVF knowledge and information sharing are inadequate among livestock farmers in Eastern Province. Therefore, vaccination and education campaigns may need to be reevaluated within the context of these trends in order to prepare for future RVF outbreaks.     

Zooplankton in the arctic Laptev Sea--feeding ecology as indicated by fatty acid composition

The fatty acid and alcohol composition of the mesozooplanktonspecies analysed indicated a diatom-based diet in late summer.For the majority of organisms investigated, an opportunisticfeeding behaviour is assumed.     

Structural arrangement and conformational dynamics of the gamma subunit of the Na+/K+-ATPase

The Na+/K+-ATPase couples the chemical energy in ATP to transport Na+ and K+ across the plasma membrane against a concentration gradient. The ion pump is composed of two mandatory subunits: the alpha subunit, which is the major catalytic subunit, and the beta subunit, which is required for proper trafficking of the complex to the plasma membrane. In some tissues, the ion pump also contains an optional third subunit, gamma, which modulates the pump activity. To examine the conformational dynamics of the gamma subunit during ion transport and its position in relation to the alpha and the beta subunits, we have used fluorescence resonance energy transfer under voltage clamp conditions. From these experiments, evidence is provided that the gamma subunit is located adjacent to the M2-M6-M9 pocket of the alpha subunit at the transmembrane-extracellular interface. We have also used fluorescence resonance energy transfer to investigate the relative movement of the three subunits as the ion pump shuttles between the two main conformational states, E1 and E2, as described by the Albers-Post scheme. The results from this study suggest that there is no relative change in distance between the alpha and gamma subunits but there is a relative change in distance between the beta and gamma subunits during the E2 to E1 transition. It was also observed that labeling the gamma subunit at specific residues with fluorophores induces a decrease in K+-induced stationary current. This result could be due to a perturbation in the K+ branch of the reaction cycle of the pump, representing a new way to inhibit the pump.