What influences selection of native phosphorelay architectures?

AbstractPhosphorelays are signal transduction circuits that combine four different phosphorylatable protein domains for sensing environmental changes and use that information to adjust cellular metabolism to the new conditions in the milieu. Five alternative circuit architectures account for more than 99% of all phosphorelay operons annotated in over 9000 fully sequenced genomes, with one of those architectures accounting for more than 72% of all cases.Here we asked if there are biological design principles that explain the selection of preferred phosphorelay architectures in nature and what might those principles be. We created several types of data-driven mathematical models for the alternative phosphorelay architectures, exploring the dynamic behavior of the circuits in concentration and parameter space, both analytically and through over 108 numerical simulations. We compared the behavior of architectures with respect to signal amplification, speed and robustness of the response, noise in the response, and transmission of environmental information to the cell.Clustering analysis of massive Monte Carlo simulations suggests that either information transmission or metabolic cost could be important in selecting the architecture of the phosphorelay. A more detailed study using models of kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1-Ypd1-Ssk1-Skn7 of Saccharomyces cerevisiae) shows that information transmission is maximized by the natural architecture of the phosphorelay. In view of this we analyze seventeen additional phosphorelays, for which protein abundance is available but kinetic parameters are not. The architectures of 16 of these are also consistent with maximization of information transmission.Our results highlight the complexity of the genotype (architecture, parameter values, and protein abundance) to phenotype (physiological output of the circuit) mapping in phosphorelays. The results also suggest that maximizing information transmission through the circuit is important in the selection of natural circuit genotypes.

Download Full-text

Maximization of information transmission influences selection of native phosphorelay architectures

PeerJ ◽

10.7717/peerj.11558 ◽

2021 ◽

Vol 9 ◽

pp. e11558

Author(s):

Rui Alves ◽

Baldiri Salvadó ◽

Ron Milo ◽

Ester Vilaprinyo ◽

Albert Sorribas

Keyword(s):

Saccharomyces Cerevisiae ◽

Signal Transduction ◽

Bacillus Subtilis ◽

Mathematical Models ◽

Information Transmission ◽

Environmental Changes ◽

Design Principles ◽

Biological Design ◽

Parameter Values ◽

Selection Of

Phosphorelays are signal transduction circuits that sense environmental changes and adjust cellular metabolism. Five different circuit architectures account for 99% of all phosphorelay operons annotated in over 9,000 fully sequenced genomes. Here we asked what biological design principles, if any, could explain selection among those architectures in nature. We began by studying kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1 of Saccharomyces cerevisiae). We find that natural circuit architecture maximizes information transmission in both cases. We use mathematical models to compare information transmission among the architectures for a realistic range of concentration and parameter values. Mapping experimentally determined phosphorelay protein concentrations onto that range reveals that the native architecture maximizes information transmission in sixteen out of seventeen analyzed phosphorelays. These results suggest that maximization of information transmission is important in the selection of native phosphorelay architectures, parameter values and protein concentrations.

Download Full-text

Studying noise immunity of radio information transmission systems with noise-like phase-shift keyed signals and synchronization delay errors

Information and Control Systems ◽

10.31799/1684-8853-2019-3-105-113 ◽

2019 ◽

pp. 105-113

Author(s):

G. N. Maltsev ◽

A. V. Evteev

Keyword(s):

Phase Shift ◽

Information Transmission ◽

Noise Immunity ◽

Tracking System ◽

Tracking Error ◽

Information Symbol ◽

Transmission Systems ◽

Synchronization System ◽

Correlation Receiver ◽

Selection Of

Introduction: Radio information transmission systems with noise-like phase-shift keyed signals based on pseudo-random sequences have potential noise immunity provided by accurately tracking the delay of the received signal in the correlation receiver. When working with moving objects, the delay of the received signal varies continuously, and the reception quality for noise-like phase-shifted signals highly depends on the synchronization system operation and on the accuracy of estimating the received signal delay by the tracking system. To ensure the required signal reception quality, it is necessary to provide an informed choice of tracking system parameters, taking into account their effects, which are the random and systematic components of the delay tracking error, on the selected noise immunity indicator.Purpose: Analyzing how the errors in tracking the delay of a received phase-shift keyed signal based on a pseudorandom sequence by the synchronization system of a radio information transmission system can affect the probability of erroneous reception of an information symbol.Results: The calculation method was used to obtain families of dependencies of the probability of erroneous reception of an information symbol on the signal-noise ratio (SNR), and the values of the random and systematic components of the delay tracking error which are normalized to the capture band of the correlation receiver. It has been shown that at a fixed SNR, the values of the random and systematic components of the delay tracking error are critical for the erroneous reception probability. In all the cases discussed, all the dependencies are characterized by a slow change of the erroneous reception probability while the synchronization errors within the area of small SNR have fixed values. As the SNR value grows, the erroneous reception probability rapidly drops. To ensure the specified signal reception quality and the reliability of the selection of information symbols and messages in a radio information transmission system with noise-like phase-manipulated signals, its synchronization system requires a joint selection of the tracking system parameters, taking into account the limitations imposed by the operating conditions and technical implementation features.Practical relevance: The obtained results can be used in noise immunity analysis of radio information transmission systems with noise-like phase-shift keyed signals in a wide range of communication conditions, and in providing technical solutions for synchronization systems ensuring the required quality of signal reception.

Download Full-text

Incorporating radiomics into clinical trials: expert consensus on considerations for data-driven compared to biologically driven quantitative biomarkers

European Radiology ◽

10.1007/s00330-020-07598-8 ◽

2021 ◽

Author(s):

Laure Fournier ◽

Lena Costaridou ◽

Luc Bidaut ◽

Nicolas Michoux ◽

Frederic E. Lecouvet ◽

...

Keyword(s):

Clinical Trials ◽

Quantitative Imaging ◽

A Priori ◽

External Validation ◽

Data Driven ◽

Imaging Biomarkers ◽

Clinical Validation ◽

Biological Processes ◽

Imaging Data ◽

Selection Of

Abstract Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. Key Points • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

Download Full-text

Adaptive selection of reference stiffness in virtual clustering analysis

Computer Methods in Applied Mechanics and Engineering ◽

10.1016/j.cma.2020.113621 ◽

2021 ◽

Vol 376 ◽

pp. 113621

Author(s):

Xi Zhu ◽

Lei Zhang ◽

Shaoqiang Tang

Keyword(s):

Clustering Analysis ◽

Adaptive Selection ◽

Virtual Clustering ◽

Selection Of

Download Full-text

Clonal selection of Eucalyptus grandis x Eucalyptus globulus for productivity, adaptability, and stability, using SNP markers

Silvae Genetica ◽

10.1515/sg-2016-0014 ◽

2016 ◽

Vol 65 (2) ◽

pp. 30-38 ◽

Cited By ~ 1

Author(s):

D. Torres-Dini ◽

A. C. P. Nunes ◽

A. Aguiar ◽

N. Nikichuk ◽

C. Centurión ◽

...

Keyword(s):

Eucalyptus Globulus ◽

Environmental Changes ◽

Clonal Selection ◽

Eucalyptus Grandis ◽

Small Population ◽

Snp Markers ◽

Hybrid Population ◽

Environment Interaction ◽

Predictive Capacity ◽

Selection Of

Abstract In Uruguay, reforestations with Eucalyptus sp. is of fundamental importance to supply paper, pulp, and wood production. This study investigates genetic, productivity, stability, and adaptability parameters in the selection of Eucalypts grandis x Eucalyptus globulus full-sib hybrid clones. The study was conducted in a clonal test, repeated in two different soils types, in Rio Negro State, Uruguay. The population was characterized phenotypically for diameter at breast height (dbh) and genotyped for SNP markers (EuCHIP60K chip). Mean dbh was similar between sites and the genotype–environment interaction was simple. We found high genotype correlation in clone performance between environments (0.708), indicating the possibility of selecting the same clones for both study locations. Mean heritability between clones (0.724), coefficient of individual genetic variation (10.9 %), and relative variation (0.916), suggest the possibility of gains (estimated at 3.1 % for both sites together) by selecting clones with higher growth rates. A total of 15,196 SNPs were used to confirm parentage and test a genomic selection model for dbh. The predictive capacity was negative (-0.15) given the small population size (78 individuals). The most adaptable material among the tested study sites presented higher values for SNP heterozygosity. Thus, using molecular markers to identify clones responsive to environmental changes can act as a powerful tool in Eucalyptus breeding programs. The hybrid population showed greater adaptability than E. globulus for this region.

Download Full-text

DEVELOPMENT OF ALTERNATIVES TO MITIGATE THE DETERIORATION OF SEGARA ANAKAN LAGOON AS REVEALED BY ANALYTICAL HIERARCHY PROCESS

Journal of the Civil Engineering Forum ◽

10.22146/jcef.26587 ◽

2017 ◽

Vol 2 (3) ◽

pp. 235

Author(s):

Harnita Rosalina

Keyword(s):

Analytical Hierarchy Process ◽

Environmental Changes ◽

Local Economy ◽

Mangrove Forests ◽

Coastal Fisheries ◽

Fisheries Resources ◽

Watershed Conservation ◽

Segara Anakan Lagoon ◽

Hierarchy Process ◽

Selection Of

Segara Anakan is a lagoon located in estuary area of Citanduy and Cibeureum rivers. The main problem that exists in the region Segara Anakan is a shrinking area of Segara Anakan lead lagoon function becomes ineffective due to the increased volume of sediment in estuaries Citanduy. Refinement Segara Anakan will impact annual floods that occurred in the area downstream Citanduy. Have far-reaching is the decline in fish production, which makes the source of livelihood for the community residents of Kampung Laut, furthermore, the environmental changes that occurred in the area Segara Anakan have resulted in shrinking coastal fisheries resources and the expansion of land arising from silting. Assessment of the problem conducted by the method of approach of Analytical Hierarchy Process(AHP) to obtain the best alternatives among three alternatives being offered to sustain the function of Segara Anakan Lagoon. These three alternatives include the 1) Dredging the Lagoon and Upstream Watershed Conservation; 2) Dredging the Lagoon and Reclamation Work around Segara Anakan, and 3) Dredging the Lagoon and Citanduy Diversion. Some criteria and sub-criteria are adapted to support the selection of the alternatives and related questionnaires were developed, and the questionnaire filling was carried out through the implementation of Focus Group of Discussion or FGD. The criteria include several aspects of the criteria and sub-criteria are technical (floods, silting), socioeconomic (the tourist area, the local economy), as well as the environment (fisheries/shipping, agriculture and mangrove forests). Results of the analysis applying the AHP method showed the consistent value on the Alternative 3), i.e. the Dredging of the Lagoon and the Upstream Watershed Conservation (38%).

Download Full-text

Selection of Pairings Reaching Evenly Across the Data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments

10.1101/009720 ◽

2014 ◽

Author(s):

Kolea Zimmerman ◽

Daniel Levitis ◽

Ethan Addicott ◽

Anne Pringle

Keyword(s):

Nearest Neighbor ◽

Simple Algorithm ◽

Two Dimensional ◽

Neighbor Distance ◽

Crossing Experiments ◽

The Mean ◽

Parameter Values ◽

Selection Of ◽

Novel Algorithm ◽

Trait Space

We present a novel algorithm for the design of crossing experiments. The algorithm identifies a set of individuals (a ?crossing-set?) from a larger pool of potential crossing-sets by maximizing the diversity of traits of interest, for example, maximizing the range of genetic and geographic distances between individuals included in the crossing-set. To calculate diversity, we use the mean nearest neighbor distance of crosses plotted in trait space. We implement our algorithm on a real dataset ofNeurospora crassastrains, using the genetic and geographic distances between potential crosses as a two-dimensional trait space. In simulated mating experiments, crossing-sets selected by our algorithm provide better estimates of underlying parameter values than randomly chosen crossing-sets.

Download Full-text

DeGreening: An Installation of Photographic Works

10.32920/ryerson.14656200 ◽

2021 ◽

Author(s):

Sadaf Pourghorbani

Keyword(s):

Land Use ◽

Land Use Change ◽

Environmental Changes ◽

Current Situation ◽

Northern Province ◽

Changing Environment ◽

Political Issues ◽

History Of ◽

Agricultural Areas ◽

Selection Of

This thesis is a supporting paper for a photographic exhibition that explores contemporary social and political issues in the country of Iran, through the depiction of a changing landscape. The work consists of photographs of the northern province of Gilan, Iran. As a critical body of work, the installation engages audiences to experience the changing environment and asks viewers to question the causes of the environmental changes in agricultural areas. A brief history of land use change in Iran during the White revolution is presented followed by a description of the current situation of farmlands in contemporary Iran. Goals for the project, methodology and issues of subjectivity are discussed. The shooting strategies, selection of the images, and presentation of the project is outlined. Finally, the essay discusses the project’s documentary relevance.

Download Full-text

The Impact of the Nocturnal Transition on the Lifetime and Evolution of Supercell Thunderstorms in the Great Plains

Weather and Forecasting ◽

10.1175/waf-d-17-0150.1 ◽

2018 ◽

Vol 33 (4) ◽

pp. 1045-1061 ◽

Cited By ~ 5

Author(s):

Matthew E. Gropp ◽

Casey E. Davenport

Keyword(s):

Thermodynamic Parameters ◽

Great Plains ◽

Environmental Changes ◽

Kinematic Parameters ◽

Storm Evolution ◽

Composite Parameter ◽

Convective Inhibition ◽

Supercell Thunderstorms ◽

Parameter Values ◽

The Impact

Abstract Predicting the evolution of supercell thunderstorms during and after the evening transition is a known challenge due to an incomplete understanding of how these events evolve in response to associated environmental changes. To quantify the connection between storm evolution and environmental changes during the nocturnal transition, 157 initially isolated Great Plains supercell thunderstorms occurring between 2005 and 2016 are examined. Each supercell is categorized as either maintained, dissipating, growing upscale, or merging. Changes in the inflow environment are quantified using hourly RUC and RAP model proximity soundings between 1 h prior to local sunset time and 5 h postsunset. Using these soundings, numerous thermodynamic and kinematic parameters are derived, and distributions of these parameter values are statistically compared among the evolution categories. It was found that each evolution classification existed in a unique set of kinematic and thermodynamic parameters; this distinction was most evident when comparing maintained and dissipation categories. In particular, storm-relative helicity, most unstable convective inhibition (MUCIN), and associated composite parameters were best able to distinguish supercell evolution. Notably, maintained supercells were characterized by significant increases in storm-relative helicity and comparatively smaller increases in the magnitude of MUCIN during the nocturnal transition; together, these parameters promote a sustained and robust rotating updraft. A convective inhibition–scaled supercell composite parameter is proposed to further assist in predicting supercell maintenance during the nocturnal transition.

Download Full-text