scholarly journals Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Camila Pontes ◽  
Miguel Andrade ◽  
José Fiorote ◽  
Werner Treptow
Keyword(s):  
Mutual Information ◽  
Three Dimensional ◽  
Type I ◽  
Sequence Alignments ◽  
Error Sources ◽  
Interacting Protein ◽  
Machine Learning Classification ◽  
Protein Partners ◽  
Signal Type ◽  
Dimensional Distribution

AbstractThe problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were shown to store the strongest mutual information (MI) signal to discriminate MSA concatenations with the largest fraction of correct pairings. Although that signal might be of practical relevance in the search for an effective heuristic to solve the problem, the number of MSA concatenations with near-native MI is large, imposing severe limitations. Here, a Genetic Algorithm that explores possible MSA concatenations according to a MI maximization criteria is shown to find degenerate solutions with two error sources, arising from mismatches among (i) similar and (ii) non-similar sequences. If mistakes made among similar sequences are disregarded, type-(i) solutions are found to resolve correct pairings at best true positive (TP) rates of 70%—far above the very same estimates in type-(ii) solutions. A machine learning classification algorithm helps to show further that differences between optimized solutions based on TP rates are not artificial and may have biological meaning associated with the three-dimensional distribution of the MI signal. Type-(i) solutions may therefore correspond to reliable results for predictive purposes, found here to be more likely obtained via MI maximization across protein systems having a minimum critical number of amino acid contacts on their interaction surfaces (N > 200).

scholarly journals Coevolutive, Evolutive and Stochastic Information in Protein-Protein Interactions

2019 ◽  
Author(s):  
Miguel Andrade ◽  
Camila Pontes ◽  
Werner Treptow
Keyword(s):  
Amino Acids ◽  
Mutual Information ◽  
Information Content ◽  
Protein Interactions ◽  
Data Sets ◽  
Binding Modes ◽  
Sources Of Information ◽  
Protein Protein Interactions ◽  
Sequence Alignments ◽  
Interacting Protein

ABSTRACTHere, we investigate the contributions of coevolutive, evolutive and stochastic information in determining protein-protein interactions (PPIs) based on primary sequences of two interacting protein families A and B. Specifically, under the assumption that coevolutive information is imprinted on the interacting amino acids of two proteins in contrast to other (evolutive and stochastic) sources spread over their sequences, we dissect those contributions in terms of compensatory mutations at physically-coupled and uncoupled amino acids of A and B. We find that physically-coupled amino-acids at short range distances store the largest per-contact mutual information content, with a significant fraction of that content resulting from coevolutive sources alone. The information stored in coupled amino acids is shown further to discriminate multi-sequence alignments (MSAs) with the largest expectation fraction of PPI matches – a conclusion that holds against various definitions of intermolecular contacts and binding modes. When compared to the informational content resulting from evolution at long-range interactions, the mutual information in physically-coupled amino-acids is the strongest signal to distinguish PPIs derived from cospeciation and likely, the unique indication in case of molecular coevolution in independent genomes as the evolutive information must vanish for uncorrelated proteins.SIGNIFICANCEThe problem of predicting protein-protein interactions (PPIs) based on multi-sequence alignments (MSAs) appears not completely resolved to date. In previous studies, one or more sources of information were taken into account not clarifying the isolated contributions of coevolutive, evolutive and stochastic information in resolving the problem. By benefiting from data sets made available in the sequence- and structure-rich era, we revisit the field to show that physically-coupled amino-acids of proteins store the largest (per contact) information content to discriminate MSAs with the largest expectation fraction of PPI matches – a result that should guide new developments in the field, aiming at characterizing protein interactions in general.

Three-dimensional distribution of ribulose-1, 5-bisphosphate carboxylase/oxygemase during the early development of proplastids in dark-grown Euglena cells transferred to an inorganic medium

1990 ◽  
Vol 48 (3) ◽  
pp. 906-907
Author(s):  
Tomoko Ehara ◽  
Shuji Sumida ◽  
Tetsuaki Osafune ◽  
Eiji Hase
Keyword(s):  
Cell Suspension ◽  
Euglena Gracilis ◽  
Carbon Materials ◽  
Three Dimensional ◽  
Peripheral Region ◽  
Plastid Development ◽  
Bisphosphate Carboxylase ◽  
Inorganic Medium ◽  
Ribulose 1 ◽  
Dimensional Distribution

As shown previously, Euglena cells grown in Hutner’s medium in the dark without agitation accumulate wax as well as paramylum, and contain proplastids showing no internal structure except for a single prothylakoid existing close to the envelope. When the cells are transferred to an inorganic medium containing ammonium salt and the cell suspension is aerated in the dark, the wax was oxidatively metabolized, providing carbon materials and energy 23 for some dark processes of plastid development. Under these conditions, pyrenoid-like structures (called “pro-pyrenoids”) are formed at the sites adjacent to the prolamel larbodies (PLB) localized in the peripheral region of the proplastid. The single prothylakoid becomes paired with a newly formed prothylakoid, and a part of the paired prothylakoids is extended, with foldings, in to the “propyrenoid”. In this study, we observed a concentration of RuBisCO in the “propyrenoid” of Euglena gracilis strain Z using immunoelectron microscopy.

scholarly journals Dip angles of active faults from the surface to the seismogenic zone inferred from a 2D numerical analysis of visco-elasto-plastic models: a case study for the Osaka Plain

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Hayami Nishiwaki ◽  
Takamoto Okudaira ◽  
Kazuhiko Ishii ◽  
Muneki Mitamura
Keyword(s):  
Urban Areas ◽  
Active Faults ◽  
Three Dimensional ◽  
Seismogenic Zone ◽  
Earthquake Ground Motion ◽  
Convex Curve ◽  
Seismic Reflection Profile ◽  
Geological Structures ◽  
Dimensional Distribution ◽  
Dip Angle

AbstractThe geometries (i.e., dip angles) of active faults from the surface to the seismogenic zone are the most important factors used to evaluate earthquake ground motion, which is crucial for seismic hazard assessments in urban areas. In Osaka, a metropolitan city in Japan, there are several active faults (e.g., the Uemachi and Ikoma faults), which are inferred from the topography, the attitude of active faults in surface trenches, the seismic reflection profile at shallow depths (less than 2 km), and the three-dimensional distribution of the Quaternary sedimentary layers. The Uemachi and Ikoma faults are N–S-striking fault systems with total lengths of 42 km and 38 km, respectively, with the former being located ~ 12 km west of the latter; however, the geometries of each of the active faults within the seismogenic zone are not clear. In this study, to examine the geometries of the Uemachi and Ikoma faults from the surface to the seismogenic zone, we analyze the development of the geological structures of sedimentary layers based on numerical simulations of a two-dimensional visco-elasto-plastic body under a horizontal compressive stress field, including preexisting high-strained weak zones (i.e., faults) and surface sedimentation processes, and evaluate the relationship between the observed geological structures of the Quaternary sediments (i.e., the Osaka Group) in the Osaka Plain and the model results. As a result, we propose geometries of the Uemachi and Ikoma faults from the surface to the seismogenic zone. When the friction coefficient of the faults is ~ 0.5, the dip angles of the Uemachi and Ikoma faults near the surface are ~ 30°–40° and the Uemachi fault has a downward convex curve at the bottom of the seismogenic zone, but does not converge to the Ikoma fault. Based on the analysis in this study, the dip angle of the Uemachi fault zone is estimated to be approximately 30°–40°, which is lower than that estimated in the previous studies. If the active fault has a low angle, the width of the fault plane is long, and thus the estimated seismic moment will be large.

scholarly journals Positive natural selection in primate genes of the type I interferon response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elena N. Judd ◽  
Alison R. Gilchrist ◽  
Nicholas R. Meyerson ◽  
Sara L. Sawyer
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Interferon Stimulated Genes ◽  
Interferon Induction

Abstract Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one. Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.

scholarly journals Simulation and measurement of air quality in the traffic congestion area

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
Shin Yu ◽  
Chang Tang Chang ◽  
Chih Ming Ma
Keyword(s):  
Air Quality ◽  
Traffic Congestion ◽  
Traffic Management ◽  
Reference Model ◽  
Dispersion Model ◽  
Fluid Model ◽  
Three Dimensional ◽  
Vehicle Speed ◽  
Management Plans ◽  
Dimensional Distribution

AbstractThe traffic congestion in the Hsuehshan tunnel and at the Toucheng interchange has led to traffic-related air pollution with increasing concern. To ensure the authenticity of our simulation, the concentration of the last 150 m in Hsuehshan tunnel was simulated using the computational fluid dynamics fluid model. The air quality at the Toucheng interchange along a 2 km length highway was simulated using the California Line Source Dispersion Model. The differences in air quality between rush hours and normal traffic conditions were also investigated. An unmanned aerial vehicle (UAV) with installed PM2.5 sensors was developed to obtain the three-dimensional distribution of pollutants. On different roads, during the weekend, the concentrations of pollutants such as SOx, CO, NO, and PM2.5 were observed to be in the range of 0.003–0.008, 7.5–15, 1.5–2.5 ppm, and 40–80 μg m− 3, respectively. On weekdays, the vehicle speed and the natural wind were 60 km h− 1 and 2.0 m s− 1, respectively. On weekdays, the SOx, CO, NO, and PM2.5 concentrations were found to be in the range of 0.002–0.003, 3–9, 0.7–1.8 ppm, and 35–50 μg m− 3, respectively. The UAV was used to verify that the PM2.5 concentrations of vertical changes at heights of 9.0, 7.0, 5.0, and 3.0 m were 45–48, 30–35, 25–30, and 50–52 μg m− 3, respectively. In addition, the predicted PM2.5 concentrations were 40–45, 25–30, 45–48, and 45–50 μg m− 3 on weekdays. These results provide a reference model for environmental impact assessments of long tunnels and traffic jam-prone areas. These models and data are useful for transportation planners in the context of creating traffic management plans.

scholarly journals Three-dimensional distribution of CT attenuation in the lumbar spine pedicle wall

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tomoyo Y. Irie ◽  
Tohru Irie ◽  
Alejandro A. Espinoza Orías ◽  
Kazuyuki Segami ◽  
Norimasa Iwasaki ◽  
...  
Keyword(s):  
Lumbar Spine ◽  
Age Groups ◽  
Three Dimensional ◽  
Hounsfield Unit ◽  
Lateral Wall ◽  
Ct Attenuation ◽  
Dimensional Distribution ◽  
The Mean ◽  
Pedicle Wall

AbstractThis study investigated in vivo the three-dimensional distribution of CT attenuation in the lumbar spine pedicle wall measured in Hounsfield Unit (HU). Seventy-five volunteers underwent clinical lumbar spine CT scans. Data was analyzed with custom-written software to determine the regional variation in pedicle wall attenuation values. A cylindrical coordinate system oriented along the pedicle’s long axis was used to calculate the pedicular wall attenuation distribution three-dimensionally and the highest attenuation value was identified. The pedicular cross-section was divided into four quadrants: lateral, medial, cranial, and caudal. The mean HU value for each quadrant was calculated for all lumbar spine levels (L1–5). The pedicle wall attenuation was analyzed by gender, age, spinal levels and anatomical quadrant. The mean HU values of the pedicle wall at L1 and L5 were significantly lower than the values between L2–4 in both genders and in both age groups. Furthermore, the medial quadrant showed higher HU values than the lateral quadrant at all levels and the caudal quadrant showed higher HU values at L1–3 and lower HU values at L4–5 than the cranial quadrant. These findings may explain why there is a higher incidence of pedicle screw breach in the pedicle lateral wall.

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