scholarly journals Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009722
Author(s):  
Jennifer T. Pentz ◽  
Peter A. Lind
Keyword(s):  
Experimental Evolution ◽  
Hot Spot ◽  
Sequence Divergence ◽  
Structural Basis ◽  
Extended Model ◽  
Short Term ◽  
Promoter Regions ◽  
Experimental Conditions ◽  
Diguanylate Cyclases ◽  
Air Liquid Interface

Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.

scholarly journals Evolutionary forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas

2018 ◽  
Author(s):  
Peter A. Lind
Keyword(s):  
Experimental Evolution ◽  
Negative Regulation ◽  
Mutation Rates ◽  
Short Term ◽  
Promoter Regions ◽  
Regulatory Pathways ◽  
Term Evolution ◽  
Upstream Promoter ◽  
Successful Prediction ◽  
Underlying Causes

AbstractExperimental evolution is often highly repeatable, but the underlying causes are generally unknown, which prevents extension of evolutionary forecasts to related species. Data on adaptive phenotypes, mutation rates and targets from the Pseudomonas fluorescens SBW25 Wrinkly Spreader system combined with mathematical models of the genotype-to-phenotype map allowed evolutionary forecasts to be made for several related Pseudomonas species. Predicted outcomes of experimental evolution in terms of phenotype, types of mutations, relative rates of pathways and mutational targets were then tested in Pseudomonas protegens Pf-5. As predicted, most mutations were found in three specific regulatory pathways resulting in increased production of Pel exopolysaccharide. Mutations were, as predicted, mainly found to disrupt negative regulation with a smaller number in upstream promoter regions. Mutated regions in proteins could also be predicted, but most mutations were not identical to those previously found. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations.Impact statementConservation of genotype-to-phenotype maps allows successful prediction of short-term evolution in P. protegens Pf-5 and lays the foundation for evolutionary forecasting in other Pseudomonas.

Structural basis of muscle O2 diffusing capacity: evidence from muscle function in situ

2000 ◽  
Vol 88 (2) ◽  
pp. 560-566 ◽  
Author(s):  
Russell T. Hepple ◽  
Michael C. Hogan ◽  
Creed Stary ◽  
Donald E. Bebout ◽  
Odile Mathieu-Costello ◽  
...  
Keyword(s):  
Gastrocnemius Muscle ◽  
Capillary Density ◽  
Structural Basis ◽  
Diffusing Capacity ◽  
Diffusion Distance ◽  
Short Term ◽  
Cross Sectional ◽  
Intact Organism ◽  
Minimal Reduction

Although evidence for muscle O2 diffusion limitation of maximal O2 uptake has been found in the intact organism and isolated muscle, its relationship to diffusion distance has not been examined. Thus we studied six sets of three purpose-bred littermate dogs (aged 10–12 mo), with 1 dog per litter allocated to each of three groups: control (C), exercise trained for 8 wk (T), or left leg immobilized for 3 wk (I). The left gastrocnemius muscle from each animal was surgically isolated, pump-perfused, and electrically stimulated to peak O2 uptake at three randomly applied levels of arterial oxygenation [normoxia, arterial[Formula: see text]([Formula: see text]) 77 ± 2 (SE) Torr; moderate hypoxia, [Formula: see text]: 33 ± 1 Torr; and severe hypoxia, [Formula: see text]: 22 ± 1 Torr]. O2 delivery (ml ⋅ min−1 ⋅ 100 g− 1) was kept constant among groups for each level of oxygenation, with O2 delivery decreasing with decreasing [Formula: see text]. O2extraction (%) was lower in I than T or C for each condition, but calculated muscle O2 diffusing capacity (Dm[Formula: see text]) per 100 grams of muscle was not different among groups. After the experiment, the muscle was perfusion fixed in situ, and a sample from the midbelly was processed for microscopy. Immobilized muscle showed a 45% reduction of muscle fiber cross-sectional area ( P < 0.05), and a resulting 59% increase in capillary density ( P < 0.05) but minimal reduction in capillary-to-fiber ratio (not significant). In contrast, capillarity was not significantly different in T vs. C muscle. The results show that a dramatically increased capillary density (and reduced diffusion distance) after short-term immobilization does not improve Dm[Formula: see text] in heavily working skeletal muscle.

A new species of Bent-toed Gecko (Squamata, Gekkonidae, Cyrtodactylus) from the Shan Plateau in eastern Myanmar (Burma)

Zootaxa ◽  
2019 ◽  
Vol 4624 (3) ◽  
pp. 301-321 ◽  
Author(s):  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
MYINT KYAW THURA ◽  
JAMIE R. OAKS ◽  
...  
Keyword(s):  
New Species ◽  
Hot Spot ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Color Pattern ◽  
Pairwise Sequence Divergence ◽  
Taxonomic Analysis ◽  
A New Species ◽  
Karst Habitats

An integrative taxonomic analysis of the Cyrtodactylus linnwayensis group of the Shan Plateau recovered two new populations from isolated karst habitats near Pinlaung Town, Shan State as a new species, C. pinlaungensis sp. nov. Cyrtodactylus pinlaungensis sp. nov. is most closely related to a clade comprising C. linnwayensis and C. ywanganensis from the western edge of the Shan Plateau approximately 90 km to the northwest. Cyrtodactylus pinlaungensis sp. nov. can be distinguished from all members of the C. linnwayensis group by a number of statistically different morphological characters, discrete color pattern differences, and its heavy tuberculation. It also bears an uncorrected pairwise sequence divergence of 5.0–7.6% from all other species combined based on the mitochondrial gene ND2 and its flanking tRNAs. The discovery of this new species on the Shan Plateau continues to underscore the fact that this region is rapidly emerging as a herpetological diversity hot-spot for Myanmar. 

Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism

2012 ◽  
Vol 446 (2) ◽  
pp. 243-251 ◽  
Author(s):  
Ivana Biljan ◽  
Gabriele Giachin ◽  
Gregor Ilc ◽  
Igor Zhukov ◽  
Janez Plavec ◽  
...  
Keyword(s):  
Prion Protein ◽  
Structural Changes ◽  
Terminal Segment ◽  
Dominant Negative ◽  
Structural Basis ◽  
Experimental Conditions ◽  
Nmr Structures ◽  
Jakob Disease ◽  
Human Prion Protein ◽  
Prion Conversion

The most common form of prion disease in humans is sCJD (sporadic Creutzfeldt–Jakob disease). The naturally occurring E219K polymorphism in the HuPrP (human prion protein) is considered to protect against sCJD. To gain insight into the structural basis of its protective influence we have determined the NMR structure of recombinant HuPrP (residues 90–231) carrying the E219K polymorphism. The structure of the HuPrP(E219K) protein consists of a disordered N-terminal tail (residues 90–124) and a well-structured C-terminal segment (residues 125–231) containing three α-helices and two short antiparallel β-strands. Comparison of NMR structures of the wild-type and HuPrPs with pathological mutations under identical experimental conditions revealed that, although the global architecture of the protein remains intact, replacement of Glu219 with a lysine residue introduces significant local structural changes. The structural findings of the present study suggest that the protective influence of the E219K polymorphism is due to the alteration of surface charge distribution, in addition to subtle structural rearrangements localized within the epitopes critical for prion conversion.

Opposite actions of caffeine and creatine on muscle relaxation time in humans

2002 ◽  
Vol 92 (2) ◽  
pp. 513-518 ◽  
Author(s):  
P. Hespel ◽  
B. Op ‘t Eijnde ◽  
M. Van Leemputte
Keyword(s):  
Relaxation Time ◽  
Exercise Test ◽  
Muscle Relaxation ◽  
Creatine Supplementation ◽  
Caffeine Intake ◽  
Short Term ◽  
Experimental Conditions ◽  
Double Blind ◽  
Musculus Quadriceps ◽  
Intermittent Contractions

The effect of creatine and caffeine supplementation on muscle torque generation and relaxation was investigated in healthy male volunteers. Maximal torque (Tmax), contraction time (CT) from 0.25 to 0.75 of Tmax, and relaxation time (RT) from 0.75 to 0.25 of Tmax were measured during an exercise test consisting of 30 intermittent contractions of musculus quadriceps (2 s stimulation, 2 s rest) that were induced by electrical stimulation. According to a double-blind randomized crossover design, subjects ( n = 10) performed the exercise test before (pretest) and after (posttest) creatine supplementation (Cr, 4 × 5 g/day, 4 days), short-term caffeine intake (Caf, 5 mg · kg−1 · day−1, 3 days), creatine supplementation + short-term caffeine intake (Cr+Caf), acute caffeine intake (ACaf, 5 mg/kg) or placebo. Compared with placebo, Cr shortened RT by ∼5% ( P < 0.05). Conversely, Caf increased RT (+∼10%, P < 0.05), in particular as RT increased because of fatigue. RT was not significantly changed by either Cr+Caf or ACaf. Tmax and CT were similar during all experimental conditions. Initial Tmax was ∼20% of voluntary maximal isometric contraction force, which was not different between treatments. It is concluded that Caf intake (3 days) prolongs muscle RT and by this action overrides the shortening of RT due to creatine supplementation.

scholarly journals AIRE's CARD Revealed, a New Structure for Central Tolerance Provokes Transcriptional Plasticity

2007 ◽  
Vol 283 (3) ◽  
pp. 1723-1731 ◽  
Author(s):  
Brian J. Ferguson ◽  
Clare Alexander ◽  
Simona W. Rossi ◽  
Ingrid Liiv ◽  
Ana Rebane ◽  
...  
Keyword(s):  
Hot Spot ◽  
Structural Basis ◽  
Central Tolerance ◽  
Aire Gene ◽  
Transcription Cofactor ◽  
Genome Wide ◽  
Regulator Protein ◽  
Specific Antigens

Developing T cells encounter peripheral self-antigens in the thymus in order to delete autoreactive clones. It is now known that the autoimmune regulator protein (AIRE), which is expressed in thymic medullary epithelial cells, plays a key role in regulating the thymic transcription of these peripheral tissue-specific antigens. Mutations in the AIRE gene are associated with a severe multiorgan autoimmune syndrome (APECED), and autoimmune reactivities are manifest in AIRE-deficient mice. Functional AIRE protein is expressed as distinct nuclear puncta, although no structural basis existed to explain their relevance to disease. In addressing the cell biologic basis for APECED, we made the unexpected discovery that an AIRE mutation hot spot lies in a caspase recruitment domain. Combined homology modeling and in vitro data now show how APECED mutations influence the activity of this transcriptional regulator. We also provide novel in vivo evidence for AIRE's association with a global transcription cofactor, which may underlie AIRE's focal, genome-wide, alteration of the transcriptome.

Short-Term Sensory Reduction Used as a Therapeutic Aid in Enhancement of Self-Concept

1978 ◽  
Vol 42 (3_suppl) ◽  
pp. 1299-1304
Author(s):  
Jon E. Bentz
Keyword(s):  
College Freshmen ◽  
Experimental Treatment ◽  
Self Concept ◽  
Significant Enhancement ◽  
Treatment Control ◽  
Short Term ◽  
Experimental Conditions ◽  
Self Rating ◽  
Sensory Environment ◽  
High Level

48 college freshmen volunteered for this investigation and were assigned to one of four experimental conditions: sensory reduction plus message, sensory reduction only, message only, or no treatment control. All subjects rated their own personalities using a modified form of the Brownfain Self-rating Inventory one day prior to and immediately following the experimental treatment. The duration of the stimulus reduction experience was 40 min. and the taped message was designed to enhance self-concept. Results indicated that the sensory reduction inhibited the enhancement of self-concept, whereas subjects who were presented the taped message in a normal sensory environment showed a significant enhancement of self-concept. It was hypothesized that the sensory reduction created a high level of anxiety which served to interfere with the effectiveness of the stimulus tape.

Uptake of Neutral Metal Complexes by a Green Alga: Influence of pH and Humic Substances

2004 ◽  
Vol 57 (10) ◽  
pp. 931 ◽  
Author(s):  
Amiel Boullemant ◽  
Bernard Vigneault ◽  
Claude Fortin ◽  
Peter G. C. Campbell
Keyword(s):  
Humic Acid ◽  
Metal Complex ◽  
Metal Complexes ◽  
Humic Substances ◽  
Low Ph ◽  
Pseudokirchneriella Subcapitata ◽  
Short Term ◽  
Experimental Conditions ◽  
Influence Of Ph ◽  
Neutral Metal

We have examined the influence of pH and a natural humic acid on the short-term uptake (<40 min) of a neutral, lipophilic metal complex by a unicellular freshwater alga, Pseudokirchneriella subcapitata. Cadmium diethyldithiocarbamate ([Cd(DDC)2]0) was used as a model lipophilic metal complex and Suwannee River Humic Acid (SRHA) was chosen as a representative aquatic humic acid (6.5 mg C L−1). Under the experimental conditions virtually all the Cd was expected to be present as the lipophilic complex ([Cd]T = 0.38 nM; [DDC] 1 μM; [Cd2+] <10−15 M; pH 7.0, 6.0, or 5.5). Uptake of [Cd(DDC)2]0 proved to be sensitive to pH changes. It was lower at pH 6.0 and 5.5 than at pH 7.0. To our knowledge, this is the first demonstration of reduced uptake of a lipophilic metal complex at low pH. The presence of SRHA also affected uptake, either by binding the lipophilic complex in solution and reducing its bioavailability (pH 7.0) or by increasing the permeability of the algal membrane (pH 5.5).

scholarly journals Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge

2007 ◽  
Vol 6 (1) ◽  
Author(s):  
Adriano V Werhli ◽  
Dirk Husmeier
Keyword(s):  
Prior Knowledge ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Reconstruction Error ◽  
Expression Data ◽  
Multiple Sources ◽  
Promoter Regions ◽  
Experimental Conditions ◽  
Microarray Expression Data ◽  
Gene Regulatory

There have been various attempts to reconstruct gene regulatory networks from microarray expression data in the past. However, owing to the limited amount of independent experimental conditions and noise inherent in the measurements, the results have been rather modest so far. For this reason it seems advisable to include biological prior knowledge, related, for instance, to transcription factor binding locations in promoter regions or partially known signalling pathways from the literature. In the present paper, we consider a Bayesian approach to systematically integrate expression data with multiple sources of prior knowledge. Each source is encoded via a separate energy function, from which a prior distribution over network structures in the form of a Gibbs distribution is constructed. The hyperparameters associated with the different sources of prior knowledge, which measure the influence of the respective prior relative to the data, are sampled from the posterior distribution with MCMC. We have evaluated the proposed scheme on the yeast cell cycle and the Raf signalling pathway. Our findings quantify to what extent the inclusion of independent prior knowledge improves the network reconstruction accuracy, and the values of the hyperparameters inferred with the proposed scheme were found to be close to optimal with respect to minimizing the reconstruction error.

scholarly journals Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Berra Erkosar ◽  
Sylvain Kolly ◽  
Jan R. van der Meer ◽  
Tadeusz J. Kawecki
Keyword(s):  
Gut Microbiota ◽  
Experimental Evolution ◽  
Nutritional Stress ◽  
Host Population ◽  
Evolutionary Adaptation ◽  
Short Term ◽  
Growth And Survival ◽  
Poor Diet ◽  
Animal Physiology ◽  
Animal Hosts

ABSTRACTNumerous studies have shown that animal nutrition is tightly linked to gut microbiota, especially under nutritional stress. InDrosophila melanogaster, microbiota are known to promote juvenile growth, development, and survival on poor diets, mainly through enhanced digestion leading to changes in hormonal signaling. Here, we show that this reliance on microbiota is greatly reduced in replicatedDrosophilapopulations that became genetically adapted to a poor larval diet in the course of over 170 generations of experimental evolution. Protein and polysaccharide digestion in these poor-diet-adapted populations became much less dependent on colonization with microbiota. This was accompanied by changes in expression levels of dFOXO transcription factor, a key regulator of cell growth and survival, and many of its targets. These evolutionary changes in the expression of dFOXO targets to a large degree mimic the response of the same genes to microbiota, suggesting that the evolutionary adaptation to poor diet acted on mechanisms that normally mediate the response to microbiota. Our study suggests that some metazoans have retained the evolutionary potential to adapt their physiology such that association with microbiota may become optional rather than essential.IMPORTANCEAnimals depend on gut microbiota for various metabolic tasks, particularly under conditions of nutritional stress, a relationship usually regarded as an inherent aspect of animal physiology. Here, we use experimental evolution in fly populations to show that the degree of host dependence on microbiota can substantially and rapidly change as the host population evolves in response to poor diet. Our results suggest that, although microbiota may initially greatly facilitate coping with suboptimal diets, chronic nutritional stress experienced over multiple generations leads to evolutionary adaptation in physiology and gut digestive properties that reduces dependence on the microbiota for growth and survival. Thus, despite its ancient evolutionary history, the reliance of animal hosts on their microbial partners can be surprisingly flexible and may be relaxed by short-term evolution.IMPORTANCEAnimals depend on gut microbiota for various metabolic tasks, particularly under conditions of nutritional stress, a relationship usually regarded as an inherent aspect of animal physiology. Here, we use experimental evolution in fly populations to show that the degree of host dependence on microbiota can substantially and rapidly change as the host population evolves in response to poor diet. Our results suggest that, although microbiota may initially greatly facilitate coping with suboptimal diets, chronic nutritional stress experienced over multiple generations leads to evolutionary adaptation in physiology and gut digestive properties that reduces dependence on the microbiota for growth and survival. Thus, despite its ancient evolutionary history, the reliance of animal hosts on their microbial partners can be surprisingly flexible and may be relaxed by short-term evolution.

Sign in / Sign up

Export Citation Format

Share Document