scholarly journals Predictive analytics of environmental adaptability in multi-omic network models

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Claudio Angione ◽  
Pietro Lió
Keyword(s):  
Codon Usage ◽  
Environmental Conditions ◽  
Metabolic Response ◽  
Predictive Analytics ◽  
Network Models ◽  
Growth Conditions ◽  
Phenotypic Traits ◽  
Bacterial Strains ◽  
Experimental Conditions ◽  
Metabolic Markers

Abstract Bacterial phenotypic traits and lifestyles in response to diverse environmental conditions depend on changes in the internal molecular environment. However, predicting bacterial adaptability is still difficult outside of laboratory controlled conditions. Many molecular levels can contribute to the adaptation to a changing environment: pathway structure, codon usage, metabolism. To measure adaptability to changing environmental conditions and over time, we develop a multi-omic model of Escherichia coli that accounts for metabolism, gene expression and codon usage at both transcription and translation levels. After the integration of multiple omics into the model, we propose a multiobjective optimization algorithm to find the allowable and optimal metabolic phenotypes through concurrent maximization or minimization of multiple metabolic markers. In the condition space, we propose Pareto hypervolume and spectral analysis as estimators of short term multi-omic (transcriptomic and metabolic) evolution, thus enabling comparative analysis of metabolic conditions. We therefore compare, evaluate and cluster different experimental conditions, models and bacterial strains according to their metabolic response in a multidimensional objective space, rather than in the original space of microarray data. We finally validate our methods on a phenomics dataset of growth conditions. Our framework, named METRADE, is freely available as a MATLAB toolbox.

scholarly journals Initiation of Biofilm Formation byPseudomonas aeruginosa 57RP Correlates with Emergence of Hyperpiliated and Highly Adherent Phenotypic Variants Deficient in Swimming, Swarming, and Twitching Motilities

2001 ◽  
Vol 183 (4) ◽  
pp. 1195-1204 ◽  
Author(s):  
Eric Déziel ◽  
Yves Comeau ◽  
Richard Villemur
Keyword(s):  
Environmental Conditions ◽  
Phase Variation ◽  
Growth Conditions ◽  
Phenotypic Traits ◽  
Liquid Cultures ◽  
Environmental Bacterium ◽  
Type Iv ◽  
Large Colony ◽  
Small Colony

ABSTRACT Pseudomonas aeruginosa is a ubiquitous environmental bacterium capable of forming biofilms on surfaces as a survival strategy. It exhibits a large variety of competition/virulence factors, such as three types of motilities: flagellum-mediated swimming, flagellum-mediated swarming, and type IV pilus-mediated twitching. A strategy frequently used by bacteria to survive changing environmental conditions is to create a phenotypically heterogeneous population by a mechanism called phase variation. In this report, we describe the characterization of phenotypic variants forming small, rough colonies that spontaneously emerged when P. aeruginosa 57RP was cultivated as a biofilm or in static liquid cultures. These small-colony (S) variants produced abundant type IV fimbriae, displayed defective swimming, swarming, and twitching motilities, and were impaired in chemotaxis. They also autoaggregated in liquid cultures and rapidly initiated the formation of strongly adherent biofilms. In contrast, the large-colony variant (parent form) was poorly adherent, homogeneously dispersed in liquid cultures, and produced scant polar fimbriae. Further analysis of the S variants demonstrated differences in a variety of other phenotypic traits, including increased production of pyocyanin and pyoverdine and reduced elastase activity. Under appropriate growth conditions, cells of each phenotype switched to the other phenotype at a fairly high frequency. We conclude that these S variants resulted from phase variation and were selectively enriched when P. aeruginosa 57RP was grown as a biofilm or in static liquid cultures. We propose that phase variation ensures the prior presence of phenotypic forms well adapted to initiate the formation of a biofilm as soon as environmental conditions are favorable.

COOPERATIVE STRATEGIES IN FORMATION OF COMPLEX BACTERIAL PATTERNS

Fractals ◽  
1995 ◽  
Vol 03 (04) ◽  
pp. 849-868 ◽  
Author(s):  
ESHEL BEN-JACOB ◽  
OFER SHOCHET ◽  
INON COHEN ◽  
ADAM TENENBAUM ◽  
ANDRAS CZIRÓK ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Cooperative Behavior ◽  
Growth Conditions ◽  
Bacterial Strains ◽  
Cooperative Strategies ◽  
Continuous Approach ◽  
Complex Patterns ◽  
Bacterial Patterns ◽  
The Individual ◽  
Generic Strategies

In nature, bacterial colonies often must cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication channels on all levels. The result is that a profusion of complex patterns are formed during growth of various bacterial strains and for different environmental conditions. Some qualitative features of the complex morphologies may be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic “feedback”. We present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. The model is an hybridization of the continuous approach (to handle chemicals’ diffusion) and the atomistic approach (each “atom” or “walker” represents 104–105 bacteria). Using the model we demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. Efficient response of the colony requires self-organization on all levels, which can be achieved only via cooperative behavior of the bacteria. It can be viewed as the action of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony) in the determination of the emerging pattern. We show that seemingly unrelated patterns can result from the employment of the same generic strategies.

scholarly journals The art of growing plants for experimental purposes: a practical guide for the plant biologist

2012 ◽  
Vol 39 (11) ◽  
pp. 821 ◽  
Author(s):  
Hendrik Poorter ◽  
Fabio Fiorani ◽  
Mark Stitt ◽  
Uli Schurr ◽  
Alex Finck ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Growth Conditions ◽  
Plant Performance ◽  
Experimental Conditions ◽  
Rooting Medium ◽  
Critical Issues ◽  
Light Quantity ◽  
Controlled Environments ◽  
Plant Biologist ◽  
Set Up

Every year thousands of experiments are conducted using plants grown under more-or-less controlled environmental conditions. The aim of many such experiments is to compare the phenotype of different species or genotypes in a specific environment, or to study plant performance under a range of suboptimal conditions. Our paper aims to bring together the minimum knowledge necessary for a plant biologist to set up such experiments and apply the environmental conditions that are appropriate to answer the questions of interest. We first focus on the basic choices that have to be made with regard to the experimental setup (e.g. where are the plants grown; what rooting medium; what pot size). Second, we present practical considerations concerning the number of plants that have to be analysed considering the variability in plant material and the required precision. Third, we discuss eight of the most important environmental factors for plant growth (light quantity, light quality, CO2, nutrients, air humidity, water, temperature and salinity); what critical issues should be taken into account to ensure proper growth conditions in controlled environments and which specific aspects need attention if plants are challenged with a certain a-biotic stress factor. Finally, we propose a simple checklist that could be used for tracking and reporting experimental conditions.

scholarly journals Naturally Occurring Ecdysteroids in Triticum aestivum L. and Evaluation of Fenarimol as a Potential Inhibitor of Their Biosynthesis in Plants

2021 ◽  
Vol 22 (6) ◽  
pp. 2855
Author(s):  
Anna Janeczko ◽  
Jana Oklestkova ◽  
Danuše Tarkowská ◽  
Barbara Drygaś
Keyword(s):  
Triticum Aestivum ◽  
Winter Wheat ◽  
Triticum Aestivum L ◽  
Growth Conditions ◽  
Animal Kingdom ◽  
Experimental Conditions ◽  
P450 Monooxygenase ◽  
Naturally Occurring ◽  
Regulatory Effects ◽  
Potential Use

Ecdysteroids (ECs) are steroid hormones originally found in the animal kingdom where they function as insect molting hormones. Interestingly, a relatively high number of these substances can also be formed in plant cells. Moreover, ECs have certain regulatory effects on plant physiology, but their role in plants still requires further study. One of the main aims of the present study was to verify a hypothesis that fenarimol, an inhibitor of the biosynthesis of ECs in the animal kingdom, also affects the content of endogenous ECs in plants using winter wheat Triticum aestivum L. as a model plant. The levels of endogenous ECs in winter wheat, including the estimation of their changes during a course of different temperature treatments, have been determined using a sensitive analytical method based on UHPLC-MS/MS. Under our experimental conditions, four substances of EC character were detected in the tissue of interest in amounts ranging from less than 1 to over 200 pg·g−1 FW: 20-hydroxyecdysone, polypodine B, turkesterone, and isovitexirone. Among them, turkesterone was observed to be the most abundant EC and accumulated mainly in the crowns and leaves of wheat. Importantly, the level of ECs was observed to be dependent on the age of the plants, as well as on growth conditions (especially temperature). Fenarimol, an inhibitor of a cytochrome P450 monooxygenase, was shown to significantly decrease the level of naturally occurring ECs in experimental plants, which may indicate its potential use in studies related to the biosynthesis and physiological function of these substances in plants.

scholarly journals Codon usage bias and environmental adaptation in microbial organisms

2021 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Principal Component ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

The Effects of Adverse Environmental Conditions on Workload

1975 ◽  
Vol 19 (3) ◽  
pp. 301-304
Author(s):  
Ann E. Martin
Keyword(s):  
Environmental Conditions ◽  
Environmental Variables ◽  
Secondary Task ◽  
The Other ◽  
Random Numbers ◽  
Performance Decrement ◽  
Experimental Conditions ◽  
Continuous Noise ◽  
Adverse Environmental Conditions ◽  
Intermittent Noise

The present study was conducted to investigate the effects of environmental conditions on visual workload. The environmental variables used were temperature, studied at levels of 45°F., WBGT, and 95°F., WBGT; and noise, studied at 83 dBA intermittent noise and 93 dBA continuous noise. Workload was defined as the amount of attention demanded from an operator as measured by performance decrement on a secondary task while performing a primary and secondary task simultaneously. The secondary task was reading random numbers, and the primary task was reading word lists. Significant differences (p<.05) were found between the control condition and all experimental conditions. The low temperature and high temperature-continuous noise conditions were significantly different from the other conditions. Noise and temperature were found to significantly increase workload (p<05).

scholarly journals Analysis of computational codon usage models and their association with translationally slow codons

2020 ◽  
Author(s):  
Gabriel Wright ◽  
Anabel Rodriguez ◽  
Jun Li ◽  
Patricia L. Clark ◽  
Tijana Milenković ◽  
...  
Keyword(s):  
Codon Usage ◽  
Computational Models ◽  
Selective Pressure ◽  
Synonymous Codon ◽  
Ground Truth ◽  
Protein Translation ◽  
Weak Correlation ◽  
Experimental Conditions ◽  
Synonymous Codons ◽  
Genome Wide

AbstractImproved computational modeling of protein translation rates, including better prediction of where translational slowdowns along an mRNA sequence may occur, is critical for understanding co-translational folding. Because codons within a synonymous codon group are translated at different rates, many computational translation models rely on analyzing synonymous codons. Some models rely on genome-wide codon usage bias (CUB), believing that globally rare and common codons are the most informative of slow and fast translation, respectively. Others use the CUB observed only in highly expressed genes, which should be under selective pressure to be translated efficiently (and whose CUB may therefore be more indicative of translation rates). No prior work has analyzed these models for their ability to predict translational slowdowns. Here, we evaluate five models for their association with slowly translated positions as denoted by two independent ribosome footprint (RFP) count experiments from S. cerevisiae, because RFP data is often considered as a “ground truth” for translation rates across mRNA sequences. We show that all five considered models strongly associate with the RFP data and therefore have potential for estimating translational slowdowns. However, we also show that there is a weak correlation between RFP counts for the same genes originating from independent experiments, even when their experimental conditions are similar. This raises concerns about the efficacy of using current RFP experimental data for estimating translation rates and highlights a potential advantage of using computational models to understand translation rates instead.

scholarly journals Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Siles ◽  
Kirsty L. Hassall ◽  
Cristina Sanchis Gritsch ◽  
Peter J. Eastmond ◽  
Smita Kurup
Keyword(s):  
Oilseed Rape ◽  
Seed Yield ◽  
Complex Trait ◽  
Growth Conditions ◽  
Phenotypic Traits ◽  
Oilseed Crop ◽  
Crop Species ◽  
Trade Offs ◽  
Whole Plant ◽  
Plant Level

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.

scholarly journals Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

mSystems ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Collin M. Timm ◽  
Kelsey R. Carter ◽  
Alyssa A. Carrell ◽  
Se-Ran Jun ◽  
Sara S. Jawdy ◽  
...  
Keyword(s):  
Plant Growth ◽  
Environmental Conditions ◽  
Bacterial Communities ◽  
Abiotic Stresses ◽  
Growth Conditions ◽  
Plant Host ◽  
Associated Bacteria ◽  
Poplar Trees

The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

DNA Interaction and Biological Activities of Heteroleptic Palladium (II) Complexes

2021 ◽  
Vol 43 (2) ◽  
pp. 227-227
Author(s):  
Muhammad Anwar Saeed Muhammad Anwar Saeed ◽  
Hizbullah Khan Hizbullah Khan ◽  
Muhammad Sirajuddin Muhammad Sirajuddin ◽  
Syed Muhammad Salman Syed Muhammad Salman
Keyword(s):  
Biological Activities ◽  
Thiobarbituric Acid ◽  
Dna Interaction ◽  
Log P ◽  
Bacterial Strains ◽  
Experimental Conditions ◽  
H2o2 Treatment ◽  
Biological Studies ◽  
Almost All ◽  
Anti Fungal

The manuscript describes the binding of DNA as well as biological studies of some mixed ligand dithiocarbamate Palladium (II) complexes (1-5). The observed compounds are of general formulae [PdCl(DT)(PR3)]. The dithiocarbamate “DT” and “PR3” groups are varied among the studied complexes as DT = bis[(2-methoxyethyl) dithiocarbamate)] (1 and 2), dibutyl dithiocarbamate (4 and 5), bis[(2-ethyl) hexyl dithiocarbamate)] (3); PR3 = triphenyl phosphine (1), benzy diphenyl phosphine (2), diphenyl-tert-butyl phpsphine (3), diphenyl-p-tolyl phosphine (4) and diphenyl-2-methoxy phenyl phosphine (5). The synthesized complexes were screened for DNA binding study via (UV Visible spectrophotometry and Viscometery) and biological activities such as anti-bacterial and anti-fungal, Molinspiration calculations and antioxidant potencies stimulated by hydrogen peroxide in human blood lymphocytes. In case of drug DNA interaction, complexes showed some sort of interaction with DNA solution. Almost all the complexes exhibited moderate antifungal and antibacterial behavior (against Gram positive and negative bacterial strains). The Molinspiration calculation study revealed that the said Pd (II) mixed complexes are biologically significant drugs having adequate molecular properties regarding drug likeness, except the log P values of complexes 3-5 because some structural adjustments must be done for enhancement of their bioavailability and hydrophilic nature. Regarding the antioxidant potential of complexes 1, 2 and 4, the H2O2 treatment of complexes violently decreased the action of antioxidant enzymes, superoxide dismutase and catalase and enhanced the level of thiobarbituric acid-reacting substances. Under experimental conditions, we conclude that all complexes act as anti-mutagens as they significantly suppress H2O2-induced oxidative damage at non-genotoxic concentrations.

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