scholarly journals Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting

2017 ◽  
Author(s):  
David Mavor ◽  
Kyle A. Barlow ◽  
Daniel Asarnow ◽  
Yuliya Birman ◽  
Derek Britain ◽  
...  
Keyword(s):  
Fitness Landscape ◽  
Nickel Chloride ◽  
Cobalt Acetate ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Sequence Conservation ◽  
Classroom Setting ◽  
Evolutionary Time ◽  
The Difference ◽  
Chemical Conditions

AbstractAlthough the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.Builds onMavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. eLife. 2016.Impact StatementWe organized a project-based course that used deep mutational scanning in multiple chemical conditions to resolve the inconsistencies between tolerance to mutations in laboratory conditions and sequence conservation over evolutionary timescales.

Calcium activity versus "calcium threshold" as the key factor in the induction of yeast flocculation in simulated industrial fermentations

1991 ◽  
Vol 37 (4) ◽  
pp. 295-303 ◽  
Author(s):  
Charlotte L. Masy ◽  
Myriam Kockerols ◽  
Michèle M. Mestdagh
Keyword(s):  
Calcium Concentration ◽  
Chelating Agents ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Free Calcium ◽  
Yeast Saccharomyces Cerevisiae ◽  
Calcium Activity ◽  
Yeast Flocculation ◽  
Key Factor ◽  
Two Parameters

Yeast flocculation is regulated by two parameters: the free-calcium activity and the "calcium threshold" or the quantity of calcium at which cells flocculate in a turbidimetric test. The study of the influence of different factors such as calcium concentration, pH, and chelating agents on flocculation has led us to put forward the following hypothesis. Flocculation occurs when the calcium threshold becomes equal to free-calcium activity, i.e., when the medium contains the exact quantity of calcium necessary for flocculation to occur. This hypothesis has been confirmed under standard laboratory culture conditions and in simulated industrial fermentations. Key words: flocculation, yeast, Saccharomyces cerevisiae, calcium induction.

scholarly journals Cyanobacterial viruses exhibit diurnal rhythms during infection

2019 ◽  
Vol 116 (28) ◽  
pp. 14077-14082 ◽  
Author(s):  
Riyue Liu ◽  
Yaxin Liu ◽  
Yue Chen ◽  
Yuanchao Zhan ◽  
Qinglu Zeng
Keyword(s):  
Gene Expression ◽  
Light Exposure ◽  
Population Level ◽  
Transcript Abundance ◽  
Mechanistic Explanation ◽  
Underlying Mechanism ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Host Cells ◽  
Diurnal Rhythms

As an adaptation to the daily light–dark (diel) cycle, cyanobacteria exhibit diurnal rhythms of gene expression and cell cycle. The light–dark cycle also affects the life cycle of viruses (cyanophages) that infect the unicellular picocyanobacteriaProchlorococcusandSynechococcus, which are the major primary producers in the oceans. For example, the adsorption of some cyanophages to the host cells depends on light, and the burst sizes of cyanophages are positively correlated to the length of light exposure during infection. Recent metatranscriptomic studies revealed transcriptional rhythms of field cyanophage populations. However, the underlying mechanism remains to be determined, as cyanophage laboratory cultures have not been shown to exhibit diurnal transcriptional rhythms. Here, we studied variation in infection patterns and gene expression ofProchlorococcusphages in laboratory culture conditions as a function of light. We found three distinct diel-dependent life history traits in dark conditions (diel traits): no adsorption (cyanophage P-HM2), adsorption but no replication (cyanophage P-SSM2), and replication (cyanophage P-SSP7). Under light–dark cycles, each cyanophage exhibited rhythmic transcript abundance, and cyanophages P-HM2 and P-SSM2 also exhibited rhythmic adsorption patterns. Finally, we show evidence to link the diurnal transcriptional rhythm of cyanophages to the photosynthetic activity of the host, thus providing a mechanistic explanation for the field observations of cyanophage transcriptional rhythms. Our study identifies that cultured viruses can exhibit diurnal rhythms during infection, which might impact cyanophage population-level dynamics in the oceans.

scholarly journals Sakurai’s Object, V605 Aql and FG Sge: An Evolutionary Sequence Revealed

2002 ◽  
Vol 187 ◽  
pp. 193-199
Author(s):  
Timothy M. Lawlor ◽  
James MacDonald
Keyword(s):  
White Dwarf ◽  
Main Sequence ◽  
Mixing Efficiency ◽  
Evolutionary Sequence ◽  
Evolutionary Time ◽  
Convective Mixing ◽  
The Difference ◽  
Born Again ◽  
First Time ◽  
Uniform Composition

AbstractWe have completed a grid of stellar evolution calculations to study the behavior of the born again phenomenon. All our evolutionary sequences begin with a uniform composition 1 M⊙ star on the pre-main sequence Hayashi phase and end on the white dwarf cooling track. We find a very late thermal pulse occurs in 10 – 15 percent of cases. Our models supply an answer to the question of why the born again stars V4334 Sgr (Sakurai’s Object) and V605 Aql have a significantly shorter evolutionary time scale than the otherwise similar born again star FG Sge. Models with low convective mixing efficiency, η = 10–4, first evolve quickly to the AGB, return to the blue, and then evolve more slowly back to the AGB for a second time before finally returning to the white dwarf cooling track. The difference in evolution time scales can then be explained by proposing that Sakurai’s Object is evolving to the AGB for the first time but FG Sge has been observed during its second return to the AGB.

scholarly journals Optical characteristics of cryoconite (surface dust) on glaciers: the relationship between light absorbency and the property of organic matter contained in the cryoconite

2002 ◽  
Vol 34 ◽  
pp. 409-414 ◽  
Author(s):  
Nozomu Takeuchi
Keyword(s):  
Organic Matter ◽  
Humic Substances ◽  
Visible Region ◽  
The Other ◽  
Optical Characteristics ◽  
The Arctic ◽  
Mineral Particles ◽  
Significant Difference ◽  
The Difference ◽  
Chemical Conditions

AbstractOptical characteristics of the cryoconite collected from nine glaciers in the Himalaya, Tibet and the Arctic (Canada and Svalbard) were analyzed. The spectral light reflectance (visible region) of the cryoconite on the six glaciers in the Arctic and the Himalayawas generally low, indicating high light absorbency (dark coloration) of the cryoconite. In contrast, the spectral reflectances of the cryoconite on the three glaciers in Tibet were significantly higher than on the other glaciers. There was no significant difference in the spectral reflectance of mineral particles contained in the cryoconite between the Tibetan and the other glaciers, indicating that the difference in the albedo of the cryoconites is not due to the mineral particles, but due to organic matter contained in the cryoconite. Chemical analysis of the organic matter in the cryoconites revealed that the light absorbency of cryoconites is due to the amount of humic substances, which are dark-colored organic substances, the residue of bacterial decomposition of organic matter. The cryoconite of the three glaciers in Tibet contained significantly smaller amounts of humic substances than that of the other glaciers, probably due to different biological or chemical conditions. Results show that the formation of the humic substances in the cryoconite affects its optical characteristics, and possibly affects the surface albedo of the glaciers.

Mesocosm study of microalgae in different weather conditions

2020 ◽  
Author(s):  
Munay Abdulqadir Alteerah ◽  
Mohammad Noor Amal Azmai ◽  
Hishamuddin Omar ◽  
Ahmad Ismail
Keyword(s):  
Species Composition ◽  
Weather Conditions ◽  
Quality Parameters ◽  
Culture Conditions ◽  
Weather Patterns ◽  
Microalgae Biomass ◽  
Chemical Conditions ◽  
Wet And Dry Cycles ◽  
And Control ◽  
Physical And Chemical

Microalgae have valuable contributions in carbon dioxide sequestration. There are no much investigations about motivation of mix microalgae productivity in outdoor cultures. This study aims to evaluate microalgae biomass production in outdoor mesocosms under different weather conditions. The experiment was done in Tilapia pond in the hatchery of fisheries of Universiti Putra Malaysia. Weather parameters were recorded daily. Microalgae seeds were obtained from Tilapia pond effluent and added to eight floating aerated mesocosms. Mesocosms were divided into four treatments. Two g triple supper phosphate: 20g Urea were used as fertilizers. Physical and chemical conditions, microalgae primary productivity and biomass, and species composition were measured every two days. Three cycles were categorized as mix, wet and dry cycles based on weather recording scores. Water quality parameters in Treatments and controls cultures showed significant variations. Primary production variables were higher in the fertilized non-sheltered mesocosms (treatment 1). Productivity variables were lower in the dry cycle and higher in the mix cycle. The highest value of fixed CO2 was (3.2) mg/L/d in treatment 1 in the mix cycle, while the lowest value was (0.11) mg/L/d in treatment 3 and control 1 in dry cycle. Changes in weather patterns are seen in the light and temperature values. Microalgae biomass was lower in dry weather conditions because of effect of high air temperature. Weather conditions and different treatments significantly influenced microalgae species composition, due to the sensitivity in some of them to different light intensities. Chlorophytes were the most abundant due to their ability to adapt with different culture conditions.

Palaeogeographic controls on palygorskite occurrence in Maastrichtian-Palaeogene sediments of the Western High Atlas and Meseta Basins (Morocco)

Clay Minerals ◽  
2014 ◽  
Vol 49 (4) ◽  
pp. 595-608 ◽  
Author(s):  
A. Knidiri ◽  
L. Daoudi ◽  
M. El Ouahabi ◽  
B. Rhouta ◽  
F. Rocha ◽  
...  
Keyword(s):  
Depositional Environment ◽  
Chemical Precipitation ◽  
X Ray Diffraction ◽  
High Atlas ◽  
X Ray ◽  
Smectite Clays ◽  
Physical Chemical ◽  
Mineralogical Characteristics ◽  
The Difference ◽  
Chemical Conditions

AbstractThe Maastrichtian-Palaeogene series of the Western High Atlas and Meseta Basins in Morocco are particularly rich in palygorskite. The present work is aimed at clarifying the genesis of palygorskite from the interbedded facies and gaining an understanding of their relationships with the depositional environment. The mineralogical characteristics of palygorskite from these series were studied by X-ray diffraction (XRD) and electron microscopy (SEM/TEM). The palygorskite content and microstructure show large geographical and stratigraphical variations in the deposits studied. The palygorskite occurrence is directly related to palaeobathymetry, since it is the dominant clay mineral in shallow marine and restricted environments. According to the morphology of palygorskite crystallites, four types of textures were distinguished. These types of palygorskite are polygenetic, formed by chemical precipitation, by the recrystallization of smectite clays or reworked by wind or water from sub-aerial environments. The difference between the two studied sub-basins with respect to palygorskite occurrence is attributed to the palaeomorphology of the hinterlands, to the tectonic differentiation and to the physical-chemical conditions of seawater.

scholarly journals Identification and Characterization of the Asperthecin Gene Cluster of Aspergillus nidulans

2008 ◽  
Vol 74 (24) ◽  
pp. 7607-7612 ◽  
Author(s):  
Edyta Szewczyk ◽  
Yi-Ming Chiang ◽  
C. Elizabeth Oakley ◽  
Ashley D. Davidson ◽  
Clay C. C. Wang ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Type I ◽  
Genes Encoding ◽  
Identification And Characterization ◽  
Normal Laboratory

ABSTRACT The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.

scholarly journals Experimental evolution recapitulates natural evolution

2000 ◽  
Vol 355 (1403) ◽  
pp. 1677-1684 ◽  
Author(s):  
H. A. Wichman ◽  
L. A. Scott ◽  
C. D. Yarber ◽  
J. J. Bull
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Experimental Evolution ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Natural Evolution ◽  
Amino Acid Variation ◽  
Experimental Line ◽  
Amino Acid Levels ◽  
A Site

Genomes of the closely related bacteriophages ϕX174 and S13 are 5386 bases long and differ at 114 nucleotides, affecting 28 amino acids. Both parental phages were adapted to laboratory culture conditions in replicate lineages and analysed for nucleotide changes that accumulated experimentally. Of the 126 experimental substitutions, 90% encoded amino–acid changes, and 62% of the substitutions occurred in parallel in more than one experimental line. Furthermore, missense changes at 12 of the experimental sites were at residues differing between the parental phages; in ten cases the ϕX174 experimental lineages were convergent with the S13 parent, or vice versa, at both the nucleotide and amino–acid levels. Convergence at a site was even obtained in both directions in three cases. These results point to a limited number of pathways taken during evolution in these viruses, and also raise the possibility that much of the amino–acid variation in the natural evolution of these viruses has been selected.

scholarly journals Adaptive Control of a Nonlinear Convertiplane under Conditions of Uncertainty

2020 ◽  
Vol 24 (3) ◽  
pp. 35-50
Author(s):  
S. F. Yatsun ◽  
O. V. Emelyanova ◽  
Andres Santiago Martinez Leon ◽  
Luis Miguel Mosquera Morocho
Keyword(s):  
Mathematical Modeling ◽  
Adaptive Control ◽  
Control System ◽  
Reference Model ◽  
Visual Contact ◽  
Hardware System ◽  
The Difference ◽  
Chemical Conditions ◽  
And Control ◽  
Physical And Chemical

Purpose of research. The article deals with the problem of monitoring water areas in order to control their physical and chemical conditions using a flying laboratory (FL) which includes an aircraft with attachable water intake equipment and a software and hardware system. A specific feature of the monitoring of surface waters is the unpredictable behavior of air and water, periodic absence of visual contact with the aircraft, the uncertainty of tricopter characteristics. Therefore, the purpose of this article is to study the parameters of the control system (CS) to meet the requirements for the accuracy of aircraft positioning in conditions of uncertainty of external parameters. Methods. Theoretical mechanics and robot mechanics methods were used to solve the set tasks. Methods for mathematical modeling of dynamic systems were used to study the patterns of convertiplane movement. Adaptive control with a reference model were used to plan and control the movement of the aircraft. Results. The use of adaptive FL motion control made it possible to ensure convergence to zero of the tracking errors i.e., the difference between the output signals and the reference model. The proposed control system gives a good result with small disturbing effects. The parameters of the regulator that ensure the quality indicators of the ACS within the specified limits are determined. Conclusion. A mathematical model was developed and mathematical modeling of the convertiplane movement under conditions of uncertainty of external influences was performed. The problem of parameter control of a convertiplane was considered when the control coefficients were available for setting. The developed algorithms in the adaptive control system made it possible to provide faster suppression of external disturbances in comparison with the traditional PID control system for the case of a linear description of the controlled object.

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