scholarly journals Experimental evidence that metapopulation structure can accelerate adaptive evolution

2021 ◽  
Author(s):  
Partha Pratim Chakraborty ◽  
Louis R Nemzer ◽  
Rees Kassen
Keyword(s):  
Spatial Structure ◽  
Adaptive Evolution ◽  
Empirical Support ◽  
Resistant Mutant ◽  
Spatial Arrangement ◽  
Industrial Applications ◽  
Beneficial Mutation ◽  
Evolutionary Forces ◽  
Mixed Network

Whether the spatial arrangement of a population influences adaptive evolution has been a long-standing question in population genetics. In contrast to standard population genetic models, evolutionary graph theory (EGT) predicts certain topologies amplify (increase) the probability that a beneficial mutation will spread in the population relative to a well-mixed population. Here, we test these predictions empirically by tracking the fixation dynamics of an antibiotic resistant mutant under positive selection as it spreads through networks of different topologies both in vitro and in silico. We show that star-like topologies involving bi-directional dispersal between a central hub and peripheral leaves can be amplifiers of selection relative to a well-mixed network, consistent with the predictions of EGT. We further show that the mechanism responsible for amplification is the reduced probability that a rare beneficial mutant will be lost due to drift when it encounters a new patch. Our results provide the first empirical support for the prediction of EGT that spatial structure can amplify the spread of a beneficial mutation and broadens the conditions under which this phenomenon is thought to occur. We also show the importance of considering the migration rate, which is not independently adjustable in most previous models. More generally, our work underscores the potential importance of spatial structure in governing adaptive evolution by showing how the interplay between spatial structure and evolutionary forces determine the fate of a beneficial mutation. It also points the way towards using network topology to amplify the effects of weakly favoured mutations under directed evolution in industrial applications.

Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects

2020 ◽  
Vol 27 (5) ◽  
pp. 400-410
Author(s):  
Valentina De Luca ◽  
Luigi Mandrich
Keyword(s):  
Gene Evolution ◽  
Sequence Divergence ◽  
High Specificity ◽  
Industrial Applications ◽  
Point Of View ◽  
Enzyme Promiscuity ◽  
Primary Activity ◽  
Starting Point ◽  
Main Activity

: Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.

scholarly journals In VitroAntibacterial Activity of NB-003 against Propionibacterium acnes

2011 ◽  
Vol 55 (9) ◽  
pp. 4211-4217 ◽  
Author(s):  
J. Pannu ◽  
A. McCarthy ◽  
A. Martin ◽  
T. Hamouda ◽  
S. Ciotti ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Propionibacterium Acnes ◽  
Resistant Mutant ◽  
Microtiter Plate ◽  
Content Type ◽  
Oil In Water ◽  
Complete Disruption ◽  
Kinetics Of ◽  
Gel Formulations

ABSTRACTNB-003 and NB-003 gel formulations are oil-in-water nanoemulsions designed for use in bacterial infections.In vitrosusceptibility ofPropionibacterium acnesto NB-003 formulations and comparator drugs was evaluated. Both NB-003 formulations were bactericidal against allP. acnesisolates, including those that were erythromycin, clindamycin, and/or tetracycline resistant. In the absence of sebum, the MIC90s/minimum bactericidal concentrations (MBC90s) for NB-003, NB-003 gel, salicylic acid (SA), and benzoyl peroxide (BPO) were 0.5/2.0, 1.0/2.0, 1,000/2,000, and 50/200 μg/ml, respectively. In the presence of 50% sebum, the MIC90s/MBC90s of NB003 and BPOs increased to 128/1,024 and 400/1,600 μg/ml, respectively. The MIC90s/MBC90s of SA were not significantly impacted by the presence of sebum. A reduction in the MBC90s for NB-003 and BPO was observed when 2% SA or 0.5% BPO was integrated into the formulation, resulting in MIC90s/MBC90s of 128/256 μg/ml for NB003 and 214/428 μg/ml for BPO. The addition of EDTA enhanced thein vitroefficacy of 0.5% NB-003 in the presence or absence of 25% sebum. The addition of 5 mM EDTA to each well of the microtiter plate resulted in a >16- and >256-fold decrease in MIC90and MBC90, yielding a more potent MIC90/MBC90of ≤1/<1 μg/ml. The kinetics of bactericidal activity of NB-003 againstP. acneswere compared to those of a commercially available product of BPO. Electron micrographs ofP. acnestreated with NB-003 showed complete disruption of bacteria. Assessment of spontaneous resistance ofP. acnesrevealed no stably resistant mutant strains.

scholarly journals Activity of Ceftazidime-Avibactam against Fluoroquinolone-Resistant Enterobacteriaceae and Pseudomonas aeruginosa

2015 ◽  
Vol 59 (6) ◽  
pp. 3059-3065 ◽  
Author(s):  
C. Pitart ◽  
F. Marco ◽  
T. A. Keating ◽  
W. W. Nichols ◽  
J. Vila
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Resistant Mutant ◽  
Fluoroquinolone Resistance ◽  
Cross Resistance ◽  
Content Type ◽  
E Coli ◽  
Microdilution Method ◽  
Broth Microdilution Method ◽  
The Impact

ABSTRACTCeftazidime-avibactam and comparator antibiotics were tested by the broth microdilution method against 200Enterobacteriaceaeand 25Pseudomonas aeruginosastrains resistant to fluoroquinolones (including strains with the extended-spectrum β-lactamase [ESBL] phenotype and ceftazidime-resistant strains) collected from our institution. The MICs and mechanisms of resistance to fluoroquinolone were also studied. Ninety-nine percent of fluoroquinolone-resistantEnterobacteriaceaestrains were inhibited at a ceftazidime-avibactam MIC of ≤4 mg/liter (using the susceptible CLSI breakpoint for ceftazidime alone as a reference). Ceftazidime-avibactam was very active against ESBLEscherichia coli(MIC90of 0.25 mg/liter), ESBLKlebsiella pneumoniae(MIC90of 0.5 mg/liter), ceftazidime-resistant AmpC-producing species (MIC90of 1 mg/liter), non-ESBLE. coli(MIC90of ≤0.125 mg/liter), non-ESBLK. pneumoniae(MIC90of 0.25 mg/liter), and ceftazidime-nonresistant AmpC-producing species (MIC90of ≤0.5 mg/liter). Ninety-six percent of fluoroquinolone-resistantP. aeruginosastrains were inhibited at a ceftazidime-avibactam MIC of ≤8 mg/liter (using the susceptible CLSI breakpoint for ceftazidime alone as a reference), with a MIC90of 8 mg/liter. Additionally, fluoroquinolone-resistant mutants from each species tested were obtainedin vitrofrom two strains, one susceptible to ceftazidime and the other a β-lactamase producer with a high MIC against ceftazidime but susceptible to ceftazidime-avibactam. Thereby, the impact of fluoroquinolone resistance on the activity of ceftazidime-avibactam could be assessed. The MIC90values of ceftazidime-avibactam for the fluoroquinolone-resistant mutant strains ofEnterobacteriaceaeandP. aeruginosawere ≤4 mg/liter and ≤8 mg/liter, respectively. We conclude that the presence of fluoroquinolone resistance does not affectEnterobacteriaceaeandP. aeruginosasusceptibility to ceftazidime-avibactam; that is, there is no cross-resistance.

scholarly journals Mutational analysis of the mRNA operator for T4 DNA polymerase.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 203-213 ◽  
Author(s):  
M D Andrake ◽  
J D Karam
Keyword(s):  
Dna Polymerase ◽  
Mutational Analysis ◽  
Bacteriophage T4 ◽  
Spatial Arrangement ◽  
Loop Sequence ◽  
Shine Dalgarno Sequence ◽  
In Vitro Effects ◽  
Rna Hairpin

Abstract Biosynthesis of bacteriophage T4 DNA polymerase is autogenously regulated at the translational level. The enzyme, product of gene 43, represses its own translation by binding to its mRNA 5' to the initiator AUG at a 36-40 nucleotide segment that includes the Shine-Dalgarno sequence and a putative RNA hairpin structure consisting of a 5-base-pair stem and an 8-base loop. We constructed mutations that either disrupted the stem or altered specific loop residues of the hairpin and found that many of these mutations, including single-base changes in the loop sequence, diminished binding of purified T4 DNA polymerase to its RNA in vitro (as measured by a gel retardation assay) and derepressed synthesis of the enzyme in vivo (as measured in T4 infections and by recombinant-plasmid-mediated expression). In vitro effects, however, were not always congruent with in vivo effects. For example, stem pairing with a sequence other than wild-type resulted in normal protein binding in vitro but derepression of protein synthesis in vivo. Similarly, a C----A change in the loop had a small effect in vitro and a strong effect in vivo. In contrast, an A----U change near the base of the hairpin that was predicted to increase the length of the base-paired stem had small effects both in vitro and in vivo. The results suggest that interaction of T4 DNA polymerase with its structured RNA operator depends on the spatial arrangement of specific nucleotide residues and is subject to modulation in vivo.

Multimerization and tubulin binding are required for the SPIRAL2 protein to localize to and stabilize microtubule minus ends

2021 ◽  
Author(s):  
YUANWEI FAN ◽  
Natasha Bilkey ◽  
Ram Dixit
Keyword(s):  
Coiled Coil ◽  
Spatial Arrangement ◽  
In Planta ◽  
Structural Determinants ◽  
Coiled Coil Domain ◽  
Tubulin Binding ◽  
And Function ◽  
Necessary And Sufficient ◽  
Basic Region

Accruing evidence points to the control of microtubule minus-end dynamics as being crucial for the spatial arrangement and function of the microtubule cytoskeleton. In plants, the SPIRAL2 (SPR2) protein has emerged as a microtubule minus-end regulator that is structurally distinct from the animal minus-end regulators. Previously, SPR2 was shown to autonomously localize to microtubule minus ends and decrease their depolymerization rate. Here, we used in vitro and in planta experiments to identify the structural determinants required for SPR2 to recognize and stabilize microtubule minus ends. We show that SPR2 contains a single N-terminal TOG domain that binds to soluble tubulin. The TOG domain, a basic region, and coiled-coil domain are necessary and sufficient to target and stabilize microtubule minus ends. We demonstrate that the coiled-coil domain mediates multimerization of SPR2 that provides avidity for microtubule binding and is essential for binding to soluble tubulin. While TOG domain-containing proteins are traditionally thought to function as microtubule plus-end regulators, our results reveal that nature has repurposed the TOG domain of SPR2 to regulate microtubule minus ends.

scholarly journals Antioxidant Potential of Sulfated Polysaccharides from Padina boryana; Protective Effect against Oxidative Stress in In Vitro and In Vivo Zebrafish Model

Marine Drugs ◽  
2020 ◽  
Vol 18 (4) ◽  
pp. 212 ◽  
Author(s):  
Thilina U. Jayawardena ◽  
Lei Wang ◽  
K. K. Asanka Sanjeewa ◽  
Sang In Kang ◽  
Jung-Suck Lee ◽  
...  
Keyword(s):  
Cell Damage ◽  
Natural Antioxidants ◽  
Industrial Applications ◽  
Water Soluble ◽  
Sulfated Polysaccharides ◽  
Ros Scavenging ◽  
Zebrafish Model ◽  
Internal Cell

Elevated levels of reactive oxygen species (ROS) damage the internal cell components. Padina boryana, a brown alga from the Maldives, was subjected to polysaccharide extraction. The Celluclast enzyme assisted extract (PBE) and ethanol precipitation (PBP) of P. boryana were assessed against hydrogen peroxide (H2O2) induced cell damage and zebra fish models. PBP which contains the majority of sulfated polysaccharides based on fucoidan, showed outstanding extracellular ROS scavenging potential against H2O2. PBP significantly declined the intracellular ROS levels, and exhibited protection against apoptosis. The study revealed PBPs’ ability to activate the Nrf2/Keap1 signaling pathway, consequently initiating downstream elements such that catalase (CAT) and superoxide dismutase (SOD). Further, ROS levels, lipid peroxidation values in zebrafish studies were declined with the pre-treatment of PBP. Collectively, the results obtained in the study suggest the polysaccharides from P. boryana might be a potent source of water soluble natural antioxidants that could be sustainably utilized in the industrial applications.

scholarly journals Marine Antibiofouling Properties of TiO2 and Ti-Cu-O Films Deposited by Aerosol-Assisted Chemical Vapor Deposition

Coatings ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 779
Author(s):  
Caroline Villardi de Oliveira ◽  
Julie Petitbois ◽  
Fabienne Faÿ ◽  
Frédéric Sanchette ◽  
Frédéric Schuster ◽  
...  
Keyword(s):  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Anatase Phase ◽  
Field Tests ◽  
Chemical Vapor ◽  
Industrial Applications ◽  
Pure Tio2 ◽  
In Vitro Tests ◽  
Tio2 Films

The actual interest in developing light-induced catalytic coatings to act as an antibiofouling alternative has recently prompted interest in the incorporation of Cu into TiO2 films, working as a visible light sensitizer catalyst. TiO2 and new Ti-Cu-O films with Cu contents ranging between 16% and 75% Cu/(Cu + Ti) are deposited by aerosol-assisted metalorganic chemical vapor deposition at a substrate temperature of 550 °C. The films are composed of TiO2 anatase phase, mixed with Cu2O when including Cu in the composition. Pure TiO2 films’ morphologies are characterized by the formation of microflower-like structures with nanometric petals, which induce a high specific surface. These features are not present in Ti-Cu-O films. A UV-Visible study revealed that the optical band gap energy decreases with increasing Cu content. Interestingly, Ti-Cu-O films presented a highly photo-catalytic activity in the orange-G degradation. Marine biofouling field tests in Lorient’s Harbor in France and in vitro tests were carried out in order to evaluate the antifouling performance of the films, revealing that topography and chemical composition can act differently on different species. Field tests revealed that TiO2 microflowers reduced the fouling coverage. Besides, Ti-Cu-O films with 16 at.% Cu presented lower fouling coverage than films containing 58 at.% Cu. In vitro tests using two diatoms (P. tricornutum and N. perminuta) showed that the spaces between microflowers play a significant role in the adhesion of diatoms: microalgae adhere less when spaces are bigger than their cells, compared to when spaces are of the same size as cells. Films containing Cu did not alter N. perminuta growth nor adhesion, while they affected P. tricornutum by lowering its growth rate and adhesion without noticeable toxicity. Indeed, Cu-Ti-O is a very promising non-toxic fouling release film for marine and industrial applications.

scholarly journals Contributions ofyap1Mutation and SubsequentatrFUpregulation to Voriconazole Resistance inAspergillus flavus

2018 ◽  
Vol 62 (11) ◽  
Author(s):  
Yuuta Ukai ◽  
Miho Kuroiwa ◽  
Naoko Kurihara ◽  
Hiroki Naruse ◽  
Tomoyuki Homma ◽  
...  
Keyword(s):  
Point Mutation ◽  
Nuclear Export ◽  
Resistance Mechanism ◽  
Resistant Mutant ◽  
Gene Replacement ◽  
Bzip Transcription Factor ◽  
Homologous Gene ◽  
Sequencing Analysis ◽  
Content Type

ABSTRACTAspergillus flavusis the second most significant pathogenic cause of invasive aspergillosis; however, its emergence risks and mechanisms of voriconazole (VRC) resistance have not yet been elucidated in detail. Here, we demonstrate that repeated exposure ofA. flavusto subinhibitory concentrations of VRCin vitrocauses the emergence of a VRC-resistant mutant with a novel resistance mechanism. The VRC-resistant mutant shows a MIC of 16 μg/ml for VRC and of 0.5 μg/ml for itraconazole (ITC). Whole-genome sequencing analysis showed that the mutant possesses a point mutation inyap1, which encodes a bZIP transcription factor working as the master regulator of the oxidative stress response, but no mutations in thecyp51genes. This point mutation inyap1caused alteration of Leu558 to Trp (Yap1Leu558Trp) in the putative nuclear export sequence in the carboxy-terminal cysteine-rich domain of Yap1. This Yap1Leu558Trpsubstitution was confirmed as being responsible for the VRC-resistant phenotype, but not for that of ITC, by the revertant to Yap1wild typewith homologous gene replacement. Furthermore, Yap1Leu558Trpcaused marked upregulation of theatrFATP-binding cassette transporter, and the deletion ofatrFrestored susceptibility to VRC inA. flavus. These findings provide new insights into VRC resistance mechanisms via a transcriptional factor mutation that is independent of thecyp51gene mutation inA. flavus.

In vitro susceptibility ofTrichophyton rubrum isolates to griseofulvin and tioconazole. Induction and isolation of a resistant mutant to both antimycotic drugs

1996 ◽  
Vol 135 (3) ◽  
pp. 141-143 ◽  
Author(s):  
Ana Lucia Fachin ◽  
Claudia Maria Leite Maffei ◽  
Nilce Maria Martinez-Rossi
Keyword(s):  
Resistant Mutant ◽  
In Vitro Susceptibility

346 BOVINE EMBRYO DEVELOPMENT AFTER IVM/IVF/IVC OF OOCYTES STORED FOR 22 H IN VARIOUS MEDIA

2007 ◽  
Vol 19 (1) ◽  
pp. 288
Author(s):  
C. Kubota ◽  
T. Kojima ◽  
T. Nagai ◽  
X. Tian ◽  
X. Yang
Keyword(s):  
Subsequent Development ◽  
Industrial Applications ◽  
Blastocyst Stage ◽  
Developmental Competence ◽  
Control Group ◽  
Bovine Embryo ◽  
Becton Dickinson ◽  
In Vitro Storage ◽  
Bovine Oocytes

The timing of IVM–IVF–IVC is restricted by the onset of oocyte maturation, and sometimes oocytes must be treated at midnight. If we could regulate the timing of IVM of oocytes without decreasing their developmental competence, the IVM–IVF–IVC system could be a more applied technology. The present study was performed to examine the effects of in vitro storage of bovine oocytes in simple media prior to maturation culture to manipulate the start of IVM. Bovine follicular fluid (bFF), Dulbecco&apos;s PBS (PBS), M199 Earle salts (M199), and Earle salts supplemented with 5 mM NaHCO3 (M199A) were used as the fundamental media, after an addition of antibiotics, for in vitro storage of bovine cumulus&ndash;oocyte complexes (COCs) collected from ovaries obtained at the slaughterhouse. The fundamental media except for bFF were supplemented with 10&percnt; fetal bovine serum (FBS) or 1 mg mL&minus;1 polyvinyl alcohol (PVA). COCs were collected from follicles (3&ndash;8 mm in diameter) and washed twice in each medium; then approximately 50 COCs were submerged in 1 mL of each medium in cryotubes (Falcon #2812, 2.5 mL; Becton Dickinson Labware, Lincoln, NJ, USA), which were stored in a container kept at 38.5&deg;C for 22 h under air-closed condition (in vitro storage: IVS). Subsequently, the stored COCs were in vitro-matured (IVM) for 22 h in M199 with 10&percnt; FBS and 20 &micro;g mL&minus;1 estradiol, fertilized (IVF), and cultured in CR1aa (IVC) for examination of their development to the blastocyst stage (Kubota et al. 1998 Mol. Reprod. Dev. 51, 281&ndash;286). Fresh oocytes without IVS were used as controls. The nuclear status of oocytes after IVS&ndash;IVM was compared to that of control oocytes by aceto-orcein stain. Their developmental rates to the blastocyst stage after IVM&ndash;IVF&ndash;IVC were compared between experimental and control groups. The experiment was repeated more than 3 times, and results were statistically analyzed using Student&apos;s t-test. When bFF and PBS supplemented with FBS or PVA were used for IVS, the rates of survived COCs after IVS and the development to the blastocyst stage after IVM&ndash;IVF&ndash;IVC (bFF (n &equals; 87): 0&percnt;, 0&percnt;; PBS/FBS (n &equals; 72): 84&percnt;, 1&percnt;; and PBS/PVA (n &equals; 81): 89&percnt;, 6&percnt;, respectively) were significantly lower than those of the control group (n &equals; 406; 97&percnt; and 29&percnt;, respectively). On the other hand, when M199A supplemented with FBS or PVA was used for IVS, the survival rate after IVS and the developmental rate to the blastocyst stage after IVS&ndash;IVM&ndash;IVF (M199A/FBS (n &equals; 97): 82&percnt;, 28&percnt;; and M199A/PVA (n &equals; 111): 98&percnt;, 31&percnt;, respectively) did not differ from those of the control group. After IVS, cumulus expansion was not seen and most of the oocyte nuclei reached the GVBD stage. These results suggest that the nuclear maturation progress of bovine oocytes can be regulated for at least 22 h in M199A without any deleterious influence on the number of oocytes surviving at an immature state after the storage and their subsequent development to the blastocyst stage after IVM&ndash;IVF&ndash;IVC. The delayed maturation allows a flexible fertilization schedule which is advantageous in research and industrial applications.

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