Unifying view of mechanical and functional hotspots across class A GPCRs

G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors' functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. \ua9 2017 Ponzoni et al

Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein

The Beclin 1 gene is a haplo-insufficient tumor suppressor and plays an essential role in autophagy. However, the molecular mechanism by which Beclin 1 functions remains largely unknown. Here we report the crystal structure of the evolutionarily conserved domain (ECD) of Beclin 1 at 1.6 Å resolution. Beclin 1 ECD exhibits a previously unreported fold, with three structural repeats arranged symmetrically around a central axis. Beclin 1 ECD defines a novel class of membrane-binding domain, with a strong preference for lipid membrane enriched with cardiolipin. The tip of a surface loop in Beclin 1 ECD, comprising three aromatic amino acids, acts as a hydrophobic finger to associate with lipid membrane, consequently resulting in the deformation of membrane and liposomes. Mutation of these aromatic residues rendered Beclin 1 unable to stably associate with lipid membrane in vitro and unable to fully rescue autophagy in Beclin 1-knockdown cells in vivo. These observations form an important framework for deciphering the biological functions of Beclin 1

Mapping Rice Fields in Urban Shanghai, Southeast China, Using Sentinel-1A and Landsat 8 Datasets

Sentinel-1A and Landsat 8 images have been combined in this study to map rice fields in urban Shanghai, southeast China, during the 2015 growing season. Rice grown in paddies in this area is characterized by wide inter-field variability in addition to being fragmented by other landuses. Improving rice classification accuracy requires the use of multi-source and multi-temporal high resolution data for operational purposes. In this regard, we first exploited the temporal backscatter of rice fields and background land-cover types at the vertical transmitted and vertical received (VV) and vertical transmitted and horizontal received (VH) polarizations of Sentinel-1A. We observed that the temporal backscatter of rice increased sharply at the early stages of growth, as opposed to the relatively uniform temporal backscatter of the other land-cover classes. However, the increase in rice backscatter is more sustained at the VH polarization, and two-class separability measures further indicated the superiority of VH over VV in discriminating rice fields. We have therefore combined the temporal VH images of Sentinel-1A with the normalized difference vegetation index (NDVI) and the modified normalized difference water index (MNDWI) derived from a single-date cloud-free Landsat 8 image. The integration of these optical indices with temporal backscatter eliminated all commission errors in the Rice class and increased overall accuracy by 5.3%, demonstrating the complimentary role of optical indices to microwave data in mapping rice fields in subtropical and urban landscapes such as Shanghai

Comparability of Red/Near-Infrared Reflectance and NDVI Based on the Spectral Response Function between MODIS and 30 Other Satellite Sensors Using Rice Canopy Spectra

Long-term monitoring of regional and global environment changes often depends on the combined use of multi-source sensor data. The most widely used vegetation index is the normalized difference vegetation index (NDVI), which is a function of the red and near-infrared (NIR) spectral bands. The reflectance and NDVI data sets derived from different satellite sensor systems will not be directly comparable due to different spectral response functions (SRF), which has been recognized as one of the most important sources of uncertainty in the multi-sensor data analysis. This study quantified the influence of SRFs on the red and NIR reflectances and NDVI derived from 31 Earth observation satellite sensors. For this purpose, spectroradiometric measurements were performed for paddy rice grown under varied nitrogen levels and at different growth stages. The rice canopy reflectances were convoluted with the spectral response functions of various satellite instruments to simulate sensor-specific reflectances in the red and NIR channels. NDVI values were then calculated using the simulated red and NIR reflectances. The results showed that as compared to the Terra MODIS, the mean relative percentage difference (RPD) ranged from −12.67% to 36.30% for the red reflectance, −8.52% to −0.23% for the NIR reflectance, and −9.32% to 3.10% for the NDVI. The mean absolute percentage difference (APD) compared to the Terra MODIS ranged from 1.28% to 36.30% for the red reflectance, 0.84% to 8.71% for the NIR reflectance, and 0.59% to 9.32% for the NDVI. The lowest APD between MODIS and the other 30 satellite sensors was observed for Landsat5 TM for the red reflectance, CBERS02B CCD for the NIR reflectance and Landsat4 TM for the NDVI. In addition, the largest APD between MODIS and the other 30 satellite sensors was observed for IKONOS for the red reflectance, AVHRR1 onboard NOAA8 for the NIR reflectance and IKONOS for the NDVI. The results also indicated that AVHRRs onboard NOAA7-17 showed higher differences than did the other sensors with respect to MODIS. A series of optimum models were presented for remote sensing data assimilation between MODIS and other sensors

Using chatbots to support EFL listening decoding skills in a fully online environment

Aural decoding skill is an important contributor to successful EFL listening comprehension. This paper first described a preliminary study involving a 12-week undergraduate flipped decoding course, based on the flipped SEF-ARCS decoding model. Although the decoding model (N = 44) was significantly more effective in supporting students’ decoding performance than a conventional decoding course (N = 36), two main challenges were reported: teacher’s excessive workload, and high requirement for the individual teacher’s decoding skills. To address these challenges, we developed a chatbot based on the self-determination theory and social presence theory to serve as a 24/7 conversational agent, and adapted the flipped decoding course to a fully online chatbot-supported learning course to reduce the dependence on the teacher. Although results revealed that the chatbot-supported fully online group (N = 46) and the flipped group (N = 43) performed equally well in decoding test, the chatbot-supported fully online approach was more effective in supporting students’ behavioral and emotional engagement than the flipped learning approach. Students’ perceptions of the chatbot-supported decoding activities were also explored. This study provides a useful pedagogical model involving the innovative use of chatbot to develop undergraduate EFL aural decoding skills in a fully online environment

A Satellite-Derived Climatological Analysis of Urban Heat Island over Shanghai during 2000–2013

The urban heat island is generally conducted based on ground observations of air temperature and remotely sensing of land surface temperature (LST). Satellite remotely sensed LST has the advantages of global coverage and consistent periodicity, which overcomes the weakness of ground observations related to sparse distributions and costs. For human related studies and urban climatology, canopy layer urban heat island (CUHI) based on air temperatures is extremely important. This study has employed remote sensing methodology to produce monthly CUHI climatology maps during the period 2000–2013, revealing the spatiotemporal characteristics of daytime and nighttime CUHI during this period of rapid urbanization in Shanghai. Using stepwise linear regression, daytime and nighttime air temperatures at the four overpass times of Terra/Aqua were estimated based on time series of Terra/Aqua-MODIS LST and other auxiliary variables including enhanced vegetation index, normalized difference water index, solar zenith angle and distance to coast. The validation results indicate that the models produced an accuracy of 1.6–2.6 °C RMSE for the four overpass times of Terra/Aqua. The models based on Terra LST showed higher accuracy than those based on Aqua LST, and nighttime air temperature estimation had higher accuracy than daytime. The seasonal analysis shows daytime CUHI is strongest in summer and weakest in winter, while nighttime CUHI is weakest in summer and strongest in autumn. The annual mean daytime CUHI during 2000–2013 is 1.0 and 2.2 °C for Terra and Aqua overpass, respectively. The annual mean nighttime CUHI is about 1.0 °C for both Terra and Aqua overpass. The resultant CUHI climatology maps provide a spatiotemporal quantification of CUHI with emphasis on temperature gradients. This study has provided information of relevance to urban planners and environmental managers for assessing and monitoring urban thermal environments which are constantly being altered by natural and anthropogenic influences

Assessing Global Ocean Wind Energy Resources Using Multiple Satellite Data

Wind energy, as a vital renewable energy source, also plays a significant role in reducing carbon emissions and mitigating climate change. It is therefore of utmost necessity to evaluate ocean wind energy resources for electricity generation and environmental management. Ocean wind distribution around the globe can be obtained from satellite observations to compensate for limited in situ measurements. However, previous studies have largely ignored uncertainties in ocean wind energy resources assessment with multiple satellite data. It is against this background that the current study compares mean wind speeds (MWS) and wind power densities (WPD) retrieved from scatterometers (QuikSCAT, ASCAT) and radiometers (WindSAT) and their different combinations with National Data Buoy Center (NDBC) buoy measurements at heights of 10 m and 100 m (wind turbine hub height) above sea level. Our results show an improvement in the accuracy of wind resources estimation with the use of multiple satellite observations. This has implications for the acquisition of reliable data on ocean wind energy in support of management policies

Propagation of conformational changes during μ-opioid receptor activation

International audienceµ-Opioid receptors (µORs) are G-protein-coupled receptors that are activated by a structurally diverse spectrum of natural and synthetic agonists including endogenous endorphin peptides, morphine and methadone. The recent structures of the μOR in inactive and agonist-induced active states (Huang et al., ref. 2) provide snapshots of the receptor at the beginning and end of a signalling event, but little is known about the dynamic sequence of events that span these two states. Here we use solution-state NMR to examine the process of μOR activation using a purified receptor (mouse sequence) preparation in an amphiphile membrane-like environment. We obtain spectra of the μOR in the absence of ligand, and in the presence of the high-affinity agonist BU72 alone, or with BU72 and a G protein mimetic nanobody. Our results show that conformational changes in transmembrane segments 5 and 6 (TM5 and TM6), which are required for the full engagement of a G protein, are almost completely dependent on the presence of both the agonist and the G protein mimetic nanobody, revealing a weak allosteric coupling between the agonist-binding pocket and the G-protein-coupling interface (TM5 and TM6), similar to that observed for the β2-adrenergic receptor. Unexpectedly, in the presence of agonist alone, we find larger spectral changes involving intracellular loop 1 and helix 8 compared to changes in TM5 and TM6. These results suggest that one or both of these domains may play a role in the initial interaction with the G protein, and that TM5 and TM6 are only engaged later in the process of complex formation. The initial interactions between the G protein and intracellular loop 1 and/or helix 8 may be involved in G-protein coupling specificity, as has been suggested for other family A G-protein-coupled receptors