scholarly journals CALIPSO-Derived Three-Dimensional Structure of Aerosol over the Atlantic Basin and Adjacent Continents

2012 ◽  
Vol 25 (19) ◽  
pp. 6862-6879 ◽  
Author(s):  
Aaron M. Adams ◽  
Joseph M. Prospero ◽  
Chidong Zhang
Keyword(s):  
South African ◽  
Three Dimensional ◽  
Global Scale ◽  
Dimensional Structure ◽  
Vertical Profiles ◽  
Transport Pathways ◽  
African Dust ◽  
Microphysical Processes ◽  
The Impact ◽  
Broad Region

Abstract Accurate modeling of the impact of aerosols on climate requires a detailed understanding of the vertical distribution of aerosols. The Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) provides continuous high-resolution vertical profiles of aerosol properties on a near-global scale. Here the CALIPSO Vertical Feature Mask is used to document the three-dimensional (3D) frequency-of-occurrence distribution of aerosols over a broad region of the Atlantic Ocean, Africa, Europe, and the Americas. The 3D distributions illustrate the seasonal cycle in the zonal and meridional variability of the vertical profiles of mineral dust, biomass-burning smoke, polluted dust (external mixture of dust and smoke), and polluted continental aerosol, and also of their emissions sources and transport pathways. Four aerosol domains stand out in the product: dust over North Africa and the Middle East and smoke over southern Africa and South America. The transport pathways of African dust and smoke over the Atlantic are evident. The intertropical convergence zone (ITCZ) plays a clear role in limiting the southward transport of North African dust and northward transport of South African smoke. Dust and smoke are mixed in the ITCZ and consequently the highest probability of polluted dust is found there, even though the probabilities of dust and smoke in this region are relatively low. The mixing of dust and pollution has significant implications for cloud microphysical processes over a broad region of the Atlantic.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

scholarly journals Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Amino Acids ◽  
2019 ◽  
Vol 51 (10-12) ◽  
pp. 1409-1431 ◽  
Author(s):  
Luigi Grassi ◽  
Chiara Cabrele
Keyword(s):  
Small Molecules ◽  
Three Dimensional ◽  
Drug Market ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Chemical Modifications ◽  
Small Molecule Drugs ◽  
And Function ◽  
The Impact

Abstract Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Two Pathogenic Gene Mutations Identified Associating with Congenital Cataract and Iris Coloboma Respectively in a Chinese Family

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Bin Li ◽  
Bin Lu ◽  
Xuewen Guo ◽  
Shenghui Hu ◽  
Guihu Zhao ◽  
...  
Keyword(s):  
Congenital Cataract ◽  
Three Dimensional ◽  
Gene Mutations ◽  
Dimensional Structure ◽  
Chinese Family ◽  
Control Group ◽  
Three Dimensional Structure ◽  
Han Ethnicity ◽  
The Family ◽  
The Impact

Purpose. To screen out pathogenic genes in a Chinese family with congenital cataract and iris coloboma. Material and Methods. A three-generation family with congenital cataract and iris coloboma from a Han ethnicity was recruited. DNA was extracted from peripheral blood samples collected from all individuals in the family. Whole exon sequencing was employed for screening the disease-causing gene mutations in the proband, and Sanger sequencing was used for other members of the family and a control group of 500 healthy individuals. Bioinformatics analysis and three-dimensional structure predictions were used to predict the impact of amino acid changes on protein structure and function. Results. The candidate genes of cataract and iris coloboma were successfully screened out. A heterozygote mutation, CRYGD c.70C>A (p.P24T), was identified as cosegregating with congenital cataracts, while another heterozygous mutation, WFS1 c.1514G>C (p.C505S), which had not been reported previously, cosegregated with congenital iris coloboma. Bioinformatic analyses and three-dimensional structure prediction proved that the three-dimensional structures of WFS1 p.C505S and CRYGD p.P24T changed markedly and may contribute significantly to iris coloboma and congenital cataract, respectively. Conclusions. We report a novel mutation, WFS1 p.C505S, and a known mutation, CRYGD p.P24T, that cosegregate with iris coloboma and congenital cataract, respectively, in a Chinese family. This is the first time the association of WFS1 p.C505S with iris coloboma has been demonstrated, although CRYGD p.P24T has been widely reported as being associated with congenital cataract, especially in the Eastern Asian population. These findings may have future therapeutic benefit for the diagnosis of iris coloboma and congenital cataract. The results may also be relevant in further studies aiming to investigate the molecular pathogenesis of iris coloboma and congenital cataract.

scholarly journals Global-scale brittle plastic rheology at the cometesimals merging of comet 67P/Churyumov–Gerasimenko

2020 ◽  
Vol 117 (19) ◽  
pp. 10181-10187
Author(s):  
Marco Franceschi ◽  
Luca Penasa ◽  
Matteo Massironi ◽  
Giampiero Naletto ◽  
Sabrina Ferrari ◽  
...  
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Global Scale ◽  
Refractory Materials ◽  
High Porosity ◽  
A Minor ◽  
The Impact ◽  
Comet 67P ◽  
Dextral Strike Slip ◽  
Minor Extent

Observations of comet nuclei indicate that the main constituent is a mix of ice and refractory materials characterized by high porosity (70–75%) and low bulk strength (10−4–10−6 MPa); however, the nature and physical properties of these materials remain largely unknown. By combining surface inspection of comet 67P/Churyumov–Gerasimenko and three-dimensional (3D) modeling of the independent concentric sets of layers that make up the structure of its two lobes, we provide clues about the large-scale rheological behavior of the nucleus and the kinematics of the impact that originated it. Large folds in the layered structure indicate that the merging of the two cometesimals involved reciprocal motion with dextral strike–slip kinematics that bent the layers in the contact area without obliterating them. Widespread long cracks and the evidence of relevant mass loss in absence of large density variations within the comet’s body testify that large-scale deformation occurred in a brittle-plastic regime and was accommodated through folding and fracturing. Comparison of refined 3D geologic models of the lobes with triaxial ellipsoids that suitably represent the overall layers arrangement reveals characteristics that are consistent with an impact between two roughly ellipsoidal cometesimals that produced large-scale axial compression and transversal elongation. The observed features imply global transfer of impact-related shortening into transversal strain. These elements delineate a model for the global rheology of cometesimals that could be possible evoking a prominent bonding action of ice and, to a minor extent, organics.

scholarly journals The Impact of Raindrop Collisional Processes on the Polarimetric Radar Variables

2014 ◽  
Vol 71 (8) ◽  
pp. 3052-3067 ◽  
Author(s):  
Matthew R. Kumjian ◽  
Olivier P. Prat
Keyword(s):  
Electromagnetic Scattering ◽  
Vertical Profiles ◽  
Polarimetric Radar ◽  
Horizontal Polarization ◽  
One Dimensional ◽  
Microphysical Process ◽  
Warm Rain ◽  
Microphysical Processes ◽  
Differential Reflectivity ◽  
The Impact

Abstract The impact of the collisional warm-rain microphysical processes on the polarimetric radar variables is quantified using a coupled microphysics–electromagnetic scattering model. A one-dimensional bin-microphysical rain shaft model that resolves explicitly the evolution of the drop size distribution (DSD) under the influence of collisional coalescence and breakup, drop settling, and aerodynamic breakup is coupled with electromagnetic scattering calculations that simulate vertical profiles of the polarimetric radar variables: reflectivity factor at horizontal polarization ZH, differential reflectivity ZDR, and specific differential phase KDP. The polarimetric radar fingerprint of each individual microphysical process is quantified as a function of the shape of the initial DSD and for different values of nominal rainfall rate. Results indicate that individual microphysical processes (collisional processes, evaporation) display a distinctive signature and evolve within specific areas of ZH–ZDR and ZDR–KDP space. Furthermore, a comparison of the resulting simulated vertical profiles of the polarimetric variables with radar and disdrometer observations suggests that bin-microphysical parameterizations of drop breakup most frequently used are overly aggressive for the largest rainfall rates, resulting in very “tropical” DSDs heavily skewed toward smaller drops.

Investigation of the Vertical Structure of Warm-Cloud Microphysical Properties Using the Cloud Evolution Diagram, CFODD, Simulated by a Three-Dimensional Spectral Bin Microphysical Model

2012 ◽  
Vol 69 (6) ◽  
pp. 2012-2030 ◽  
Author(s):  
Yousuke Sato ◽  
Takashi Y. Nakajima ◽  
Teruyuki Nakajima
Keyword(s):  
Vertical Structure ◽  
Three Dimensional ◽  
Global Scale ◽  
Observation Data ◽  
Time Step ◽  
Microphysical Properties ◽  
Warm Cloud ◽  
Dominant Process ◽  
Microphysical Processes ◽  
Cloud Evolution

Abstract This paper investigates the vertical structure of warm-cloud microphysical properties using a three-dimensional (3D) spectral bin microphysical model. A time series of contoured frequency by optical depth diagrams (CFODDs), which were proposed by previous studies, are calculated for the first time by a 3D model assuming two types of aerosol conditions (i.e., polluted and pristine). This contrasts with previous studies that obtained CFODDs using either a two-dimensional model or an accumulation of monthly and global observation data. The results show that the simulated CFODDs are characterized by distinctive patterns of radar reflectivities, similar to the patterns often observed by satellite remote sensing, even though the calculation domain of this study is limited to an area of 30 × 30 km2, whereas the satellite observations are of a global scale. A cloud microphysical box model is then applied to the simulated cloud field at each time step to identify the dominant process for each of the patterns. The results reveal that the wide variety of satellite-observed CFODD patterns can be attributed to different microphysical processes occurring in multiple cloud cells at various stages of the cloud life cycle.

scholarly journals WaveRange: wavelet-based data compression for three-dimensional numerical simulations on regular grids

2022 ◽  
Author(s):  
Dmitry Kolomenskiy ◽  
Ryo Onishi ◽  
Hitoshi Uehara
Keyword(s):  
Numerical Simulations ◽  
Wavelet Decomposition ◽  
Three Dimensional ◽  
Global Scale ◽  
Software Framework ◽  
Simulation Data ◽  
Numerical Tests ◽  
Point Data ◽  
Dimensional Simulation ◽  
The Impact

Abstract A wavelet-based method for compression of three-dimensional simulation data is presented and its software framework is described. It uses wavelet decomposition and subsequent range coding with quantization suitable for floating-point data. The effectiveness of this method is demonstrated by applying it to example numerical tests, ranging from idealized configurations to realistic global-scale simulations. The novelty of this study is in its focus on assessing the impact of compression on post-processing and restart of numerical simulations. Graphical abstract

scholarly journals Novel biological implication of a strictly monomorphic GCC repeat in the human PRKACB gene

2021 ◽  
Author(s):  
Safoura Khamse ◽  
Zahra Jafarian ◽  
Ali Bozorgmehr ◽  
Mostafa Tavakoli ◽  
Hossein Afshar Iranian ◽  
...  
Keyword(s):  
Late Onset ◽  
Human Subjects ◽  
Three Dimensional ◽  
Dna Structure ◽  
Dimensional Structure ◽  
Protein Coding ◽  
Three Dimensional Structure ◽  
Significant Divergence ◽  
The Impact ◽  
The Brain

Abstract Across human protein-coding genes, PRKACB (Protein Kinase CAMP-Activated Catalytic Subunit Beta) contains one of the longest GCC-repeats, and is predominantly expressed in the brain. Here we studied this STR in 300 human subjects, consisting of late-onset neurocognitive disorder (NCD) (N = 150) and controls (N = 150). We also studied the impact of this STR on the three-dimensional structure of DNA. While the PRKACB GCC-STR was strictly monomorphic at 7-repeats, we detected two 7/8 genotypes only in the NCD group. In comparison to all other lengths, (GCC)7 had the least effect on the three-dimensional structure of DNA, evidenced by minimal divergence between 0 and 7-repeats (divergence score = 0.04) and significant divergence between 0 and 8 repeats (divergence score = 0.50). A similar inert effect to the GCC-repeat was not detected in other classes of STRs such as GA and CA repeats. In conclusion, we report monomorphism of an exceptionally long GCC repeat in the PRKACB gene in human, its inert effect on DNA structure, and divergence in two cases of late-onset NCD. This is the first indication of natural selection for an exceptionally long monomorphic GCC-repeat, which probably evolved to function as an “epigenetic knob”, without changing the regional DNA structure.

scholarly journals Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

2021 ◽  
Vol 17 (8) ◽  
pp. e1009284
Author(s):  
Xianggen Liu ◽  
Yunan Luo ◽  
Pengyong Li ◽  
Sen Song ◽  
Jian Peng
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Protein Design ◽  
Protein Structures ◽  
Three Dimensional ◽  
Point Mutations ◽  
Dimensional Structure ◽  
Gradient Boosting ◽  
Benchmark Datasets ◽  
The Impact

Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial role in protein engineering and drug design. In this study, we develop GeoPPI, a novel structure-based deep-learning framework to predict the change of binding affinity upon mutations. Based on the three-dimensional structure of a protein, GeoPPI first learns a geometric representation that encodes topology features of the protein structure via a self-supervised learning scheme. These representations are then used as features for training gradient-boosting trees to predict the changes of protein-protein binding affinity upon mutations. We find that GeoPPI is able to learn meaningful features that characterize interactions between atoms in protein structures. In addition, through extensive experiments, we show that GeoPPI achieves new state-of-the-art performance in predicting the binding affinity changes upon both single- and multi-point mutations on six benchmark datasets. Moreover, we show that GeoPPI can accurately estimate the difference of binding affinities between a few recently identified SARS-CoV-2 antibodies and the receptor-binding domain (RBD) of the S protein. These results demonstrate the potential of GeoPPI as a powerful and useful computational tool in protein design and engineering. Our code and datasets are available at: https://github.com/Liuxg16/GeoPPI.

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