VoroMQA: Assessment of protein structure quality using interatomic contact areas

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge‐based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue‐residue or atom‐atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation‐based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single‐model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa . Proteins 2017; 85:1131–1145. © 2017 Wiley Periodicals, Inc.     

Potential use of weather radar to study movements of wintering waterfowl

To protect and restore wintering waterfowl habitat, managers require knowledge of routine wintering waterfowl movements and habitat use. During preliminary screening of Doppler weather radar data we observed biological movements consistent with routine foraging flights of wintering waterfowl known to occur near Lacassine National Wildlife Refuge (NWR), Louisiana. During the winters of 2004–2005 and 2005–2006, we conducted field surveys to identify the source of the radar echoes emanating from Lacassine NWR. We compared field data to weather radar reflectivity data. Spatial and temporal patterns consistent with foraging flight movements appeared in weather radar data on all dates of field surveys. Dabbling ducks were the dominant taxa flying within the radar beam during the foraging flight period. Using linear regression, we found a positive log-linear relationship between average radar reflectivity (Z) and number of birds detected over the study area (P < 0.001, r² = 0.62, n = 40). Ground observations and the statistically significant relationship between radar data and field data confirm that Doppler weather radar recorded the foraging flights of dabbling ducks. Weather radars may be effective tools for wintering waterfowl management because they provide broad-scale views of both diurnal and nocturnal movements. In addition, an extensive data archive enables the study of wintering waterfowl response to habitat loss, agricultural practices, wetland restoration, and other research questions that require multiple years of data. © 2011 The Wildlife Society.     

The solid–liquid phase diagrams of binary mixtures of consecutive, even saturated fatty acids

For the first time, the solid–liquid phase diagrams of five binary mixtures of saturated fatty acids are here presented. These mixtures are formed of caprylic acid (C_8:0) + capric acid (C_10:0), capric acid (C_10:0) + lauric acid (C_12:0), lauric acid (C_12:0) + myristic acid (C_14:0), myristic acid (C_14:0) + palmitic acid (C_16:0) and palmitic acid (C_16:0) + stearic acid (C_18:0). The information used in these phase diagrams was obtained by differential scanning calorimetry (DSC), X-ray diffraction (XRD), FT–Raman spectrometry and polarized light microscopy, aiming at a complete understanding of the phase diagrams of the fatty acid mixtures. All of the phase diagrams reported here presented the same global behavior and it was shown that this was far more complex than previously imagined. They presented not only peritectic and eutectic reactions, but also metatectic reactions, due to solid–solid phase transitions common in fatty acids and regions of solid solution not previously reported. This work contributes to the elucidation of the phase behavior of these important biochemical molecules, with implications in various industrial applications.     

Solid Tryptophan as a Pseudoracemate: Physicochemical and Crystallographic Characterization

The crystalline nature of solid tryptophan has been characterized by X‐ray single crystal and powder diffraction analyses, differential scanning calorimetry, as well as measurement of solid–liquid equilibrium in water/isopropanol solution. Both the thermodynamic and crystallographic investigations have demonstrated unambiguously that solid tryptophan crystallizes in the form of a pseudoracemate (i.e., solid solution) with maximum melting over the entire enantiomeric composition range. Comparative single‐crystal X‐ray studies show that the crystal structures of racemic and enantiomeric tryptophan give very similar solid‐state packing geometries dictated by hydrogen bonding interactions. Our results indicate that the insignificant difference between homochiral and heterochiral interactions accounts for the formation of a pseudoracemate for this system. Chirality 27:88–94, 2015. © 2014 Wiley Periodicals, Inc.     

Mixed monolayers of dipalmitoylglycerophosphocholine,distearoylglycerophosphocholine and 1-palmitoylglycerol

Mixed monolayer systems of dipalmitoylglycerophosphocholine (DPPC)-distearoylglycerophosphocholine (DSPC), palmitoylglycerol-DPPC, and palmitoylglycerol-DSPC have been investigated by a previously described thermodynamic treatment. The surface pressures of these systems were measured at various compositions and temperatures. The two-dimensional phase diagrams and the apparent molar entropy and energy changes were evaluated. It was found that the phase diagrams of the DPPC-DSPC, palmitoylglycerol-DSPC and palmitoylglycerol-DPPC systems are all of different types. According to our phase diagram classification, DPPC-DSPC, palmitoylglycerol-DSPC, and palmitoylglycerol-DPPC systems exhibited a modified cigar type, a eutectic type, and a negative azeotropic type, respectively.     

Using multitemporal digital elevation model data for detecting canopy gaps in tropical forests due to cyclone damage: An initial assessment

Abstract The detection and mapping of canopy disturbance caused by natural events such as cyclones in tropical rainforests is important for monitoring and understanding rainforest dynamics and recovery. In February 1999 tropical cyclone Rona crossed the coastline of Far North Queensland, Australia, causing significant damage to the rainforest canopy in some areas. This paper examines the application of multitemporal canopy digital elevation models (DEMs) generated by a NASA‐operated airborne radar mapping system called TOPSAR in 1996 and 2000, for detection of canopy disturbance caused by cyclone damage. Canopy damage was mapped here by identifying areas with a significant decrease in canopy height estimated from the difference of the 1996 and 2000 TOPSAR DEMs. Conventional aerial photographs, flown shortly after the cyclone (March 1999), were used to validate the resulting map of cyclone damaged rainforest canopy. The results showed that the DEM‐derived canopy damage map performed reasonably well when comparing the spatial distribution and size of damaged areas, while taking into account the time difference between cyclone damage and the second radar acquisition. Some errors were encountered on the steeper slopes which were related to terrain distortions inherent in radar images of steep terrain. The height accuracy of the DEM was close to the depth of some of the gaps being mapped, which also contributed to errors. Even so, the results demonstrate there may be potential for weather‐independent, regional‐scale mapping of forest canopy change from imaging radar that is not always possible from traditional optical means of measuring canopy elevation, for example, airborne laser data and stereo aerial photography. This may be possible in relatively flat areas, provided the second radar acquisition occurs within months of the damaging event. Further algorithm refinement is required to improve its robustness and the range of topographies where this approach can provide reliable estimates of the extent of canopy disturbance.     

The steppes and deserts of the Xizang Plateau (Tibet)

The Xizang Plateau (Tibet) covers a vast area over 4 000 m with a severe environment. Steppes and deserts are widely distributed on the plateau to the west of 91.5°E. Poaceae, Asteraceae, Fabaceae and Cyperaceae are the most important families in the composition of steppe communities. The steppe can be divided into high-cold steppe and montane steppe. The former one is characterized by the Stipa purpurea community, which occupies a vast area with a cold, dry climate: annual mean temperature 0 to –6°C, annual rainfall is 150–300 mm; The latter one is distributed in some limited regions, where the climate is less severe: annual mean temperature 0–7°C, annual rainfall is 150–400 mm. The representative communities here are the Stipa glareosa and S. bungeana communities. Chenopodiaceae and Asteraceae play a principal role in both high-cold and montane deserts. The high-cold desert is unique. Its major representative is the Ceratoides compacta community, which is found at about 5 000 m, in an extremely cold and very dry climate. The Ceratoides latens and Ajania fruticulosa communities are the common ones of the montane desert which mainly appears below 4 600 m in elevation, where the annual temperature is about 0°C and the rainfall is less than 100 mm. The distribution of the steppe and the desert communities shows a clear regional differentiation, and an equally clear vertical distribution pattern.     

Ongoing changes in migration phenology and winter residency at Bracken Bat Cave

Bats play an important role in agroecology and are effective bioindicators of environmental conditions, but little is known about their fundamental migration ecology, much less how these systems are responding to global change. Some of the world's largest bat populations occur during the summer in the south‐central United States, when millions of pregnant females migrate from lower latitudes to give birth in communal maternity colonies. Despite a relatively large volume of research into these colonies, many fundamental questions regarding their abundance—including their intra‐ and interseasonal variability—remain unanswered, and even estimating the size of individual populations has been a long‐running challenge. Overall, monitoring these bat populations at high temporal resolution (e.g., nightly) and across long time spans (e.g., decades) has been impossible. Here, we show 22 continuous years of nightly population counts at Bracken Cave, a large bat colony in south‐central Texas, enabling the first climate‐scale phenological analysis. Using quantitative radar monitoring, we found that spring migration and the summer reproductive cycle have advanced by approximately 2 weeks over the study period. Furthermore, we quantify the ongoing growth of a newly—established overwintering population that indicates a system‐wide response to changing environmental conditions. Our observations reveal behavioral plasticity in bats’ ability to adapt to changing resource availability, and provide the first long‐term quantification of their response to a changing climate. As aerial insectivores, these changes in bat phenology and propensity for overwintering indicate probable shifts in prey availability, with clear implications for pest management across wider regional agrisystems.     

Thermotropism and hydration properties of POPE and POPE-cholesterol systems as revealed by solid state2H and31P-NMR

The partial phase diagram and the hydration properties of the 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE)-water system, in the absence and presence of 30 mol% cholesterol, have been investigated by solid state phosphorus NMR of the lipid and deuterium NMR of heavy water. The POPE-D₂O phase diagram resembles other phosphatidylethanolamine (PE)-water systems: below water-to-lipid molar ratios (R_i) of 3 the lamellar gel (L or L_c)-to-hexagonal type II (H_II) phase sequence is observed on increasing the temperature. For R_i3 the thermotropic sequence (L or L_c)-L-H_II is detected. On increasing hydration from R_i=3, the H_II phase is detected from 40°C to 85°C whereas the gel phase is observed from 40°C to 30°C. The limiting hydrations of the gel, L and H_II phases are R_i 3, 17 and 20, respectively. The number of bound water molecules per lipid is ca. 8 in both the La and HII phases. The presence of cholesterol stabilizes the hexagonal phase 20°C below temperatures at which it is observed in its absence and reduces the limiting hydration of the fluid and hexagonal phases to Ri 9 and 14, respectively. The structure and/or dynamics of the water bound to the interface are markedly modified on going from the L to the H_II phase.Abbreviations NMR Nuclear magnetic resonance - DDPE 1,2-Didodecyl-rac-glycerol-3-phosphoethanol-amine - DHPE 1,2-Dihexadecyl-sn-glycerol-3-phosphoethanol-amine - DOPE 1,2-Dioleoyl-sn-glycerol-3-phosphoethanol-amine - POPE 1-Palmitoyl-2-oleoyl-sn-glycerol-3-phosphoetha-nolamine - DAPE 1,2-Diarachinoyl-sn-glycerol-3-phosphoethanol-amine - DMPC 1,2-Dimyristol-sn-glycerol-3-phosphocholine - DPPC 1,2-Dipalmitoyl-sn-glycerol-3-phosphocholine - T_c lamellar gel-to-lamellar fluid transition temperature - T_h lamellar fluid-to-hexagonal transition temperature     

Effects of organic pH buffers on a cell growth and an antibody production of human-human hybridoma HB4C5 cells in a serum-free culture

Human-human hybridoma cells secreting a human monoclonal antibody were cultured in a serum-free medium containing various organic pH buffers in order to clarify their effects on cell growth and antibody production. Organic pH buffers having either one sulfonic acid and several acyclic amine moieties, or several cyclic amine moieties containing two amino nitrogen did not inhibit cell growth; while other organic buffers sulfonic acid moiety plus several cyclic amine moieties containing one amino nitrogen slightly decreased cell growth, but enhanced antibody production. Using Fujita's organic conceptual diagram, a relationship between the organicity and inorganicity of a pH buffer to cell growth and antibody production was found. pH buffers with large inorganicity and small organicity values were favorable for cell growth, and buffers with small inorganicity and large organicity values were preferred to enhance antibody production. Although the pH buffering range affects cell growth, its effect on antibody production is not clear. In conclusion, 2-morpholinoethanesulfonic acid (MES), 3-morpholino-propanesulfonic acid (MOPS) and 1, 2-N, N-bis[N, N-di(2-sulfonoethyl)piperazinyl]ethane (Bis-PIPES) are shown to be the most optimal of the buffers tested, because they enhanced antibody production without decreasing the cell growth among the pH buffers tested here.