Thermal Adaptation of Conformational Dynamics in Ribonuclease H

The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. In particular, ribonuclease HI (RNase H), an 18 kD globular protein that hydrolyzes the RNA strand of RNA:DNA hybrid substrates, has been extensively studied by NMR spectroscopy to characterize the differences in dynamics between homologs from the mesophilic organism E. coli and the thermophilic organism T. thermophilus. Herein, molecular dynamics simulations are reported for five homologous RNase H proteins of varying thermostabilities and enzymatic activities from organisms of markedly different preferred growth temperatures. For the E. coli and T. thermophilus proteins, strong agreement is obtained between simulated and experimental values for NMR order parameters and for dynamically averaged chemical shifts, suggesting that these simulations can be a productive platform for predicting the effects of individual amino acid residues on dynamic behavior. Analyses of the simulations reveal that a single residue differentiates between two different and otherwise conserved dynamic processes in a region of the protein known to form part of the substrate-binding interface. Additional key residues within these two categories are identified through the temperature-dependence of these conformational processes.     

Seasonal and Geographic Variation of Southern Blue Whale Subspecies in the Indian Ocean

Understanding the seasonal movements and distribution patterns of migratory species over ocean basin scales is vital for appropriate conservation and management measures. However, assessing populations over remote regions is challenging, particularly if they are rare. Blue whales (Balaenoptera musculus spp) are an endangered species found in the Southern and Indian Oceans. Here two recognized subspecies of blue whales and, based on passive acoustic monitoring, four “acoustic populations” occur. Three of these are pygmy blue whale (B.m. brevicauda) populations while the fourth is the Antarctic blue whale (B.m. intermedia). Past whaling catches have dramatically reduced their numbers but recent acoustic recordings show that these oceans are still important habitat for blue whales. Presently little is known about the seasonal movements and degree of overlap of these four populations, particularly in the central Indian Ocean. We examined the geographic and seasonal occurrence of different blue whale acoustic populations using one year of passive acoustic recording from three sites located at different latitudes in the Indian Ocean. The vocalizations of the different blue whale subspecies and acoustic populations were recorded seasonally in different regions. For some call types and locations, there was spatial and temporal overlap, particularly between Antarctic and different pygmy blue whale acoustic populations. Except on the southernmost hydrophone, all three pygmy blue whale acoustic populations were found at different sites or during different seasons, which further suggests that these populations are generally geographically distinct. This unusual blue whale diversity in sub-Antarctic and sub-tropical waters indicates the importance of the area for blue whales in these former whaling grounds.     

Robots with Display Screens: A Robot with a More Humanlike Face Display Is Perceived To Have More Mind and a Better Personality

It is important for robot designers to know how to make robots that interact effectively with humans. One key dimension is robot appearance and in particular how humanlike the robot should be. Uncanny Valley theory suggests that robots look uncanny when their appearance approaches, but is not absolutely, human. An underlying mechanism may be that appearance affects users’ perceptions of the robot’s personality and mind. This study aimed to investigate how robot facial appearance affected perceptions of the robot’s mind, personality and eeriness. A repeated measures experiment was conducted. 30 participants (14 females and 16 males, mean age 22.5 years) interacted with a Peoplebot healthcare robot under three conditions in a randomized order: the robot had either a humanlike face, silver face, or no-face on its display screen. Each time, the robot assisted the participant to take his/her blood pressure. Participants rated the robot’s mind, personality, and eeriness in each condition. The robot with the humanlike face display was most preferred, rated as having most mind, being most humanlike, alive, sociable and amiable. The robot with the silver face display was least preferred, rated most eerie, moderate in mind, humanlikeness and amiability. The robot with the no-face display was rated least sociable and amiable. There was no difference in blood pressure readings between the robots with different face displays. Higher ratings of eeriness were related to impressions of the robot with the humanlike face display being less amiable, less sociable and less trustworthy. These results suggest that the more humanlike a healthcare robot’s face display is, the more people attribute mind and positive personality characteristics to it. Eeriness was related to negative impressions of the robot’s personality. Designers should be aware that the face on a robot’s display screen can affect both the perceived mind and personality of the robot.     

Discovery of TAK-960: An orally available small molecule inhibitor of polo-like kinase 1 (PLK1)

Using structure-based drug design, we identified and optimized a novel series of pyrimidodiazepinone PLK1 inhibitors resulting in the selection of the development candidate TAK-960. TAK-960 is currently undergoing Phase I evaluation in adult patients with advanced solid malignancies.     

High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in Argentina, Chile, China, Mexico and the USA between 2009 and 2012. We collated spore mat ITS sequences with 105 fruit body and 47 EcM root sequences to generate operational taxonomic units (OTUs). Phylogenetic inferences were made through analyses of both molecular data sets. A total of 48 OTUs from spore mats represented six independent EcM Pezizales lineages and included truffles and cup fungi. Three clades of seven OTUs have no known meiospore stage. Mitospores failed to germinate on sterile media, or form ectomycorrhizas on Quercus, Pinus and Populus seedlings, consistent with a hypothesized role of spermatia. The broad geographic range, high frequency and phylogenetic diversity of spore mats produced by EcM Pezizales suggests that a mitospore stage is important for many species in this group in terms of mating, reproduction and/or dispersal.     

Reported electronic cigarette use among adolescents in the Niagara region of Ontario

Background:Use of electronic cigarettes (e-cigarettes) among adolescents has not been fully described, in particular their motivations for using them and factors associated with use. We sought to evaluate the frequency, motivations and associated factors for e-cigarette use among adolescents in Ontario.Methods:We conducted a cross-sectional study in the Niagara region of Ontario, Canada, involving universal screening of students enrolled in grade 9 in co-operation with the Heart Niagara Inc. Healthy Heart Schools’ Program (for the 2013–2014 school year). We used a questionnaire to assess cigarette, e-cigarette and other tobacco use, and self-rated health and stress. We assessed household income using 2011 Canadian census data by matching postal codes to census code.Results:Of 3312 respondents, 2367 answered at least 1 question in the smoking section of the questionnaire (1274 of the 2367 respondents [53.8%] were male, with a mean [SD] age of 14.6 [0.5] yr) and 2292 answered the question about use of e-cigarettes. Most respondents to the questions about use of e-cigarettes (n = 1599, 69.8%) had heard of e-cigarettes, and 380 (23.8%) of these respondents had learned about them from a store sign or display. Use of e-cigarettes was reported by 238 (10.4%) students. Most of the respondents who reported using e-cigarettes (171, 71.9%) tried them because it was “cool/fun/new,” whereas 14 (5.8%) reported using them for smoking reduction or cessation. Male sex, recent cigarette or other tobacco use, family members who smoke and friends who smoke were strongly associated with reported e-cigarette use. Reported use of e-cigarettes was associated with self-identified fair/poor health rating (odds ratio [OR] 1.9 (95% confidence interval [CI] 1.2–3.0), p < 0.001), high stress level (OR 1.7 (95% CI 1.1–2.7), p < 0.001) and lower mean (33.4 [8.4] × $1000 v. 36.1 [10.7] × $1000, p = 0.001) and median [interquartile range] (26.2 [5.6] × $1000 v. 28.1 [5.7] × $1000) household incomes.Interpretation:Use of e-cigarettes is common among adolescents in the Niagara region and is associated with sociodemographic features. Engaging in seemingly exciting new behaviours appears to be a key motivating factor rather than smoking cessation.Electronic cigarettes (e-cigarettes) are novel devices that are designed to mimic the physical and tactile experience of conventional cigarettes while producing a smoke-free vapour. They have quickly gained popularity despite limited evidence regarding the health risks associated with their use and a lack of regulation.¹ In addition, existing literature about e-cigarettes suggests that they may not be effective for achieving smoking reduction or cessation, a use for which they are often marketed.^1–3 Given their physical similarities to conventional cigarettes, there are concerns that the increasing use of e-cigarettes may result in the “renormalization” of cigarette smoking.^4,5 Previous studies have suggested that use of e-cigarettes among adolescents and young adults may be associated with use of and exposure to tobacco.^1,6,7Rates of the use of e-cigarettes at least once among high school students in the United States have increased annually.^6,8 Among adolescents in Canada, use of e-cigarettes is now more common than cigarette use.⁹ However, questions still remain regarding the motivations and factors associated with e-cigarette use among adolescents. Therefore, we sought to evaluate the frequency, motivations and associated factors for use of e-cigarettes by students in grade 9 who were undergoing universal school-based screening for cardiovascular risk factors in the Niagara region in Ontario.     

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of confident peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic Saccharomyces cerevisiae dataset, and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach.     

High-throughput assays for botulinum neurotoxin proteolytic activity: serotypes A, B, D, and F

Botulinum neurotoxins (BoNT) are zinc metalloproteases that cleave and inactivate cellular proteins essential for neurotransmitter release. Because the paralytic effect of BoNT is a consequence of its enzymatic activity, selective inhibitors may be useful as drugs or as tools for further research. To expedite inhibitor discovery, we developed high-throughput, solid-phase protease activity assays for four of the seven BoNT serotypes: A, B, D, and F. Each assay consisted of a cleavable oligopeptide, based on the natural substrate sequence, labeled with fluorescein and covalently attached to maleimide-activated multiwell plates. Solutions of holotoxin or nontoxic catalytic domain of BoNT were incubated in substrate-coated wells, with or without test compounds, followed by transfer and assay of solubilized product in a multiwell fluorometer. Routine toxin concentrations ranged from 10 to 100 ng/ml, but concentrations as low as 2 ng/ml gave reproducible signals. The fluorescence assays were selective, gave very low background readings, and were stable upon prolonged storage. Using the nontoxic catalytic domain of BoNT A, we determined the relative inhibitory potencies of a family of structurally related pseudotripeptide compounds. Unlike previous methods, our assays did not employ antibodies or reverse-phase extraction steps, only well-to-well transfers, and were easily adapted to a high-throughput automated environment.     

The metal ion binding properties of calreticulin modulate its conformational flexibility and thermal stability

Calreticulin (CRT) is a soluble chaperone involved in the conformational maturation of glycoproteins in the endoplasmic reticulum. Using biochemical and biophysical techniques including circular dichroism, proteolysis, and analytical ultracentrifugation, we have determined the effects of calcium and zinc ions on the structural properties of human CRT. Circular dichroism analysis has shown that the binding of calcium and zinc ions to CRT induces no significant changes in the secondary structure of the protein but affects in very distinct ways the local tertiary packing of these elements. More specifically, these studies have revealed that CRT adopts a more rigid and thermally stable structure upon binding calcium ions and a more loosely packed and thermally destabilized structure upon binding zinc ions. Consistent with these results, proteolysis experiments demonstrated that the intrinsic conformational flexibility of CRT can be modulated toward either a decrease or an increase in susceptibility to cleavage by chymotrypsin upon binding calcium or zinc ions, respectively. Results from sedimentation analysis indicated that the global three-dimensional structure of CRT is essentially unchanged upon binding calcium ions. In marked contrast, CRT self-associates reversibly to form dimers upon binding zinc ions. Collectively, our results provide evidence that calcium and zinc ions induce strikingly different changes in the biochemical and structural properties of CRT.