scholarly journals Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Maren Wehrs ◽  
Mitchell G. Thompson ◽  
Deepanwita Banerjee ◽  
Jan-Philip Prahl ◽  
Norma M. Morella ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Population Dynamics ◽  
Bioreactor Cultivation ◽  
Study Population ◽  
Deletion Library

scholarly journals Loss of the Homotypic Fusion and Vacuole Protein Sorting or Golgi-Associated Retrograde Protein Vesicle Tethering Complexes Results in Gentamicin Sensitivity in the Yeast Saccharomyces cerevisiae

2006 ◽  
Vol 50 (2) ◽  
pp. 587-595 ◽  
Author(s):  
Mark C. Wagner ◽  
Elizabeth E. Molnar ◽  
Bruce A. Molitoris ◽  
Mark G. Goebl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Intracellular Trafficking ◽  
Protein Sorting ◽  
Growth Conditions ◽  
Yeast Saccharomyces Cerevisiae ◽  
Vesicle Tethering ◽  
Yeast Deletion Library ◽  
Texas Red ◽  
Deletion Library ◽  
Logarithmic Growth

ABSTRACT Gentamicin continues to be a primary antibiotic against gram-negative infections. Unfortunately, associated nephro- and ototoxicity limit its use. Our previous mammalian studies showed that gentamicin is trafficked to the endoplasmic reticulum in a retrograde manner and subsequently released into the cytosol. To better dissect the mechanism through which gentamicin induces toxicity, we have chosen to study its toxicity using the simple eukaryote Saccharomyces cerevisiae. A recent screen of the yeast deletion library identified multiple gentamicin-sensitive strains, many of which participate in intracellular trafficking. Our approach was to evaluate gentamicin sensitivity under logarithmic growth conditions. By quantifying growth inhibition in the presence of gentamicin, we determined that several of the sensitive strains were part of the Golgi-associated retrograde protein (GARP) and homotypic fusion and vacuole protein sorting (HOPS) complexes. Further evaluation of their other components showed that the deletion of any GARP member resulted in gentamicin-hypersensitive strains, while the deletion of other HOPS members resulted in less gentamicin sensitivity. Other genes whose deletion resulted in gentamicin hypersensitivity included ZUO1, SAC1, and NHX1. Finally, we utilized a Texas Red gentamicin conjugate to characterize gentamicin uptake and localization in both gentamicin-sensitive and -insensitive strains. These studies were consistent with our mammalian studies, suggesting that gentamicin toxicity in yeast results from alterations to intracellular trafficking pathways. The identification of genes whose absence results in gentamicin toxicity will help target specific pathways and mechanisms that contribute to gentamicin toxicity.

scholarly journals Population dynamics of Saccharomyces cerevisiae PE-2 and CAT-1 in CO-culture for the production of ethanol

2020 ◽  
Vol 42 ◽  
pp. e43427
Author(s):  
Mayara Vieira Santos ◽  
Adriana Régia Marques Souza ◽  
Maria Carolina Santos Silva ◽  
Gabriel Luis Castiglioni
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Population Dynamics ◽  
Acetic Acid ◽  
Ethanol Production ◽  
Metabolic Pathways ◽  
The Other ◽  
Yeast Strains ◽  
Pure Cultures ◽  
Fermentation Monitoring ◽  
Biotechnological Processes

In the Brazilian industries, the inoculum used throughout the harvest of ethanol production consists of a combination of two or more yeast strains. The combination of yeasts may influence in the metabolic pathways of microorganisms and increase the yields and production rates of some compounds. In biotechnological processes with co-culture, one microorganism can prevail over the other. Therefore, the knowledge about how the population dynamics occurs during fermentation allows modifications in the process in order to obtain higher yields and to achieve greater fermentative efficiency. The aim of this study was to investigate the fermentation with synthetic sugar cane broth in co-culture of Saccharomyces cerevisiae strains CAT-1 and PE-2 followed by molecular fermentation monitoring. The concentration of biomass, ethanol, glycerol, acetic acid and residual sucrose were monitored to verify the influence of different combinations during the fermentation. The mixture of CAT-1 and PE-2 presented the highest ethanol production, with higher performance of fermentative parameters than pure cultures

scholarly journals PREDATOR–PREY MODEL WITH AGE STRUCTURE

2017 ◽  
Vol 59 (2) ◽  
pp. 155-166
Author(s):  
J. PROMRAK ◽  
G. C. WAKE ◽  
C. RATTANAKUL
Keyword(s):  
Population Dynamics ◽  
Predator Prey ◽  
Predator Prey Model ◽  
Green Lacewings ◽  
Cassava Plant ◽  
Age Dependent ◽  
Important Pest ◽  
Mckendrick Equation ◽  
Study Population ◽  
The Stability

Mealybug is an important pest of cassava plant in Thailand and tropical countries, leading to severe damage of crop yield. One of the most successful controls of mealybug spread is using its natural enemies such as green lacewings, where the development of mathematical models forecasting mealybug population dynamics improves implementation of biological control. In this work, the Sharpe–Lotka–McKendrick equation is extended and combined with an integro-differential equation to study population dynamics of mealybugs (prey) and released green lacewings (predator). Here, an age-dependent formula is employed for mealybug population. The solutions and the stability of the system are considered. The steady age distributions and their bifurcation diagrams are presented. Finally, the threshold of the rate of released green lacewings for mealybug extermination is investigated.

scholarly journals Detection, Diversity, and Population Dynamics of Waterborne Phytophthora ramorum Populations

2015 ◽  
Vol 105 (1) ◽  
pp. 57-68 ◽  
Author(s):  
C. A. Eyre ◽  
M. Garbelotto
Keyword(s):  
Population Dynamics ◽  
Pathogen Detection ◽  
Phytophthora Ramorum ◽  
Natural Forests ◽  
Tree Disease ◽  
The United Kingdom ◽  
Risk Areas ◽  
Study Population ◽  
Polymerase Chain ◽  
Stream Baiting

Sudden oak death, the tree disease caused by Phytophthora ramorum, has significant environmental and economic impacts on natural forests on the U.S. west coast, plantations in the United Kingdom, and in the worldwide nursery trade. Stream baiting is vital for monitoring and early detection of the pathogen in high-risk areas and is performed routinely; however, little is known about the nature of water-borne P. ramorum populations. Two drainages in an infested California forest were monitored intensively using stream-baiting for 2 years between 2009 and 2011. Pathogen presence was determined both by isolation and polymerase chain reaction (PCR) from symptomatic bait leaves. Isolates were analyzed using simple sequence repeats to study population dynamics and genetic structure through time. Isolation was successful primarily only during spring conditions, while PCR extended the period of pathogen detection to most of the year. Water populations were extremely diverse, and changed between seasons and years. A few abundant genotypes dominated the water during conditions considered optimal for aerial populations, and matched those dominant in aerial populations. Temporal patterns of genotypic diversification and evenness were identical among aerial, soil, and water populations, indicating that all three substrates are part of the same epidemiological cycle, strongly influenced by rainfall and sporulation on leaves. However, there was structuring between substrates, likely arising due to reduced selection pressure in the water. Additionally, water populations showed wholesale mixing of genotypes without the evident spatial autocorrelation present in leaf and soil populations.

scholarly journals Seasonal variation of genotypes and reproductive plasticity in a facultative clonal freshwater invertebrate animal (Hydra oligactis) living in a temperate lake

2021 ◽  
Author(s):  
Mate Miklos ◽  
Levente Laczko ◽  
Gabor Sramko ◽  
Zoltan Barta ◽  
Jacint Tokolyi
Keyword(s):  
Population Dynamics ◽  
Population Biology ◽  
Freshwater Ecosystems ◽  
Phenotypic Data ◽  
Genetic Changes ◽  
Invertebrate Animal ◽  
Sexual And Asexual Reproduction ◽  
Freshwater Invertebrate ◽  
Long Time ◽  
Study Population

Facultative sexual organisms combine sexual and asexual reproduction within a single life cycle, often switching between reproductive modes depending on environmental conditions. These organisms frequently inhabit variable seasonal environments, where favourable periods alternate with unfavourable periods, generating temporally varying selection pressures that strongly influence life history decisions and hence population dynamics. Due to the rapidly accelerating changes in our global environment today, understanding the dynamics of and genetic changes in facultative sexual populations inhabiting seasonal environments is critical to assess and prepare for additional challenges that will affect such ecosystems. In this study we aimed at obtaining insights of the seasonal population dynamics of the facultative sexual freshwater cnidarian Hydra oligactis through a combination of Restriction-site Associated Sequencing (RAD-Seq) genotyping and the collection of phenotypic data on the reproductive strategy of field-collected hydra strains. We found no significant genetic change during the two years in the study population. Clone lines were detected between seasons and even years, suggesting that clonal lineages can persist for a long time in a natural population. We also found that distinct genotypes differ in sexual reproduction frequency, but these differences did not affect whether genotypes reappeared across samplings. Our study describes changes in population genetic structure across the seasons in a hydra population for the first time, providing key insights into the biology of the species, while also contributing to understanding the population biology of facultative sexual species inhabiting freshwater ecosystems.

scholarly journals Cryptic density dependence: effects of spatio-temporal covariation between density and site quality in reef fish

2020 ◽  
Author(s):  
Jeffrey Shima ◽  
C Osenberg
Keyword(s):  
Population Dynamics ◽  
Density Dependence ◽  
Reef Fish ◽  
Site Quality ◽  
Central Importance ◽  
Density Dependent ◽  
Density Dependent Mortality ◽  
Study Population ◽  
Spatio Temporal ◽  
Thalassoma Hardwicke

The importance and strength of density dependence continues to engender debate because of its central importance to population dynamics and regulation. Here, we show how confounding effects of site quality can mask strong effects of density dependence. In particular, we explore spatiotemporal variation and covariation among (1) densities of newly settled coral reef fish (Thalassoma hardwicke), (2) environmental characteristics, and (3) the strength of density-dependent mortality. Environmental features of patch reefs were spatially and temporally variable and influenced density-dependent survival. Higher-quality sites (i.e., reefs possessing features that yield greater numbers of recruits at any given settlement level) received greater settlement, and this relationship masked the operation of density dependence when variation in quality among sites (or times) was not distinguished (a common approach in many Observational studies of density dependence). Our work illustrates how spatiotemporal covariation in settlement density and site quality can obscure patterns of density dependence at larger scales, contributing to a phenomenon we call "cryptic density dependence." Acknowledging patterns and consequences of covariance may alter the way we study population dynamics, especially of marine organisms, where the link between processes that affect settlement and post-settlement survival remains relatively poorly understood.

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