scholarly journals Large-scale rewiring in a yeast hybrid

2017 ◽  
Author(s):  
Rebecca H. Herbst ◽  
Dana Bar-Zvi ◽  
Sharon Reikhav ◽  
Ilya Soifer ◽  
Michal Breker ◽  
...  
Keyword(s):  
Large Scale ◽  
Growth Conditions ◽  
Cell Cycle Checkpoints ◽  
Hybrid Vigor ◽  
Ethanol Stress ◽  
Regulatory Processes ◽  
Parental Background ◽  
Hybrid Growth ◽  
Growing Conditions ◽  
Yeast Hybrid

AbstractThe merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. We describe a budding yeast hybrid that grows faster than its parents under different environments. Phenotypically, the hybrid progresses more rapidly through cell cycle checkpoints, relieves the repression of respiration in fast growing conditions, does not slow down its growth when presented with ethanol stress, and shows increasing signs of DNA damage. A systematic genetic screen identified hundreds of alleles affecting hybrid growth whose identity vastly differed between the hybrid and its parent and between growth conditions. This large-scale rewiring of allele effects suggests that despite showing clear heterosis, the hybrid is perturbed in multiple regulatory processes. We discuss the possibility that incompatibilities contribute to hybrid vigor by perturbing safeguard mechanisms that limit growth in the parental background.

scholarly journals Bioactive Compounds, Antioxidant Activity and Growth Behavior in Lettuce Cultivars Grown under Field and Greenhouse Conditions

Proceedings ◽  
2020 ◽  
Vol 70 (1) ◽  
pp. 52
Author(s):  
Melisa Lanza Volpe ◽  
Verónica C. Soto Vargas ◽  
Anabel Morón ◽  
Roxana E. González
Keyword(s):  
Antioxidant Activity ◽  
Bioactive Compounds ◽  
Antioxidant Activities ◽  
Growth Conditions ◽  
Growth Behavior ◽  
Total Phenolic ◽  
Spectrophotometric Methods ◽  
Leafy Greens ◽  
Growing Conditions ◽  
Field Production

Lettuce (Lactuca sativa L.) is one of the most important leafy greens worldwide. The nutritional value of its edible leaf depends on different factors including type and growing conditions. The aim was to determine the bioactive compounds content, antioxidant activity and growth behavior of twenty-two lettuce genotypes, cultivated under field and greenhouse conditions. Total phenolic compound, chlorophylls, carotenoids, anthocyanin contents and antioxidant activities were analyzed by spectrophotometric methods. Data were analyzed by analysis of variance (ANOVA). Significant differences between bioactive compounds, antioxidant activity and growth behavior were found among cultivars and morphological types, for both growth conditions. Carotenoid and chlorophyll content was higher in greenhouse conditions for all genotypes. In field production, butterhead and iceberg lettuces showed lower content of these bioactive compounds. The red-pigmented Falbala cultivar from field production showed the highest level of polyphenols and anthocyanin. Meanwhile, in greenhouse conditions, the oak leaf cultivar Grenadine displayed the highest concentration of these phenolic compounds. The iceberg type lettuce showed the lowest percentages of antioxidant activity in both environments. The results showed the effect of growing conditions and the high variability in lettuce bioactive compounds content and antioxidant activity among the different types.

scholarly journals Xanthones Production in Gentiana dinarica Beck Hairy Root Cultures Grown in Simple Bioreactors

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1610
Author(s):  
Branka Vinterhalter ◽  
Nevena Banjac ◽  
Dragan Vinterhalter ◽  
Dijana Krstić-Milošević
Keyword(s):  
Hairy Root ◽  
Large Scale ◽  
Bubble Column ◽  
Growth Parameters ◽  
Growth Index ◽  
Dry Weight ◽  
Growth Conditions ◽  
Good Growth ◽  
Gentiana Dinarica ◽  
Hairy Root Clones

The hairy root clones of Gentiana dinarica cl-B, cl-D, cl-3, and cl-14 were cultivated in parallel in diverse simple bioreactors, including temporary immersion systems RITA® (TIS RITA®), bubble column bioreactors (BCB), and Erlenmeyer flasks (EF), and evaluated for biomass production and xanthone content. The obtained results showed that TIS RITA® and BCB containing ½ MS medium with 4% sucrose provided equally good growth conditions in which the majority of the clones displayed the higher percentage of dry matter (DM%), and xanthones norswertianin-1-O-primeveroside (nor-1-O-prim) and norswertianin production than those cultivated in EF. Thin and well branched hairy root clone cl-B grown in BCB for 7 weeks was superior regarding all growth parameters tested, including growth index (19.97), dry weight (2.88 g), and DM% (25.70%) compared to all other clones. Cl-B cultured in TIS RITA® contained the highest amount of nor-1-O-prim (56.82 mg per vessel). In BCB with constant aeration, cl-B accumulated the highest norswertianin content reaching 18.08 mg/vessel. The optimized conditions for cultivation of selected G. dinarica hairy root clones in highly aerated TIS RITA® and BCB systems contribute to the development of bioreactor technology designed for the large scale commercial production of xanthones nor-1-O-prim and norswertianin.

Large-scale prediction of aboveground biomass in heterogeneous mountain forests by means of airborne laser scanning

2016 ◽  
Vol 46 (9) ◽  
pp. 1138-1144 ◽  
Author(s):  
M. Maltamo ◽  
O.M. Bollandsås ◽  
T. Gobakken ◽  
E. Næsset
Keyword(s):  
Aboveground Biomass ◽  
Laser Scanning ◽  
Large Scale ◽  
Airborne Laser Scanning ◽  
Mountain Forests ◽  
Airborne Laser ◽  
Model Predictions ◽  
Growing Conditions ◽  
Southern Norway ◽  
Forest Conditions

This study considered airborne laser scanning (ALS) based aboveground biomass (AGB) prediction in mountain forests. The study area consisted of a long transect from southern Norway to northern parts of the country with wide ranges of elevation along a long latitudinal gradient (58°N–69°N). This transect was covered by ALS data and field data from 238 plots. AGB was modeled using different types of predictor variables, namely ALS metrics, variables related to growing conditions (elevation, latitude, and climatic variables), and tree species information. Modelling of AGB in the long transect covering diverse mountainous forest conditions was challenging: the RMSE values were rather large (37%–70%). The effects of growing conditions on model predictions were minor. However, species information was essential to improve accuracy. The analysis revealed that when doing inventories of spruce-dominated areas, all plots should be pooled together when the models are developed, whereas if pine or deciduous species dominate the area in question, separate dominant species-wise models should be constructed.

scholarly journals Resonant Mixing in Glass Bowl Microbioreactor Investigated by Microparticle Image Velocimetry

Micromachines ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 284 ◽  
Author(s):  
Sven Meinen ◽  
Lasse Jannis Frey ◽  
Rainer Krull ◽  
Andreas Dietzel
Keyword(s):  
Surface Waves ◽  
Growth Conditions ◽  
Capillary Surface ◽  
Mixing Conditions ◽  
Glass Slides ◽  
Image Velocimetry ◽  
Resonance Frequencies ◽  
Microparticle Image Velocimetry ◽  
Growing Conditions ◽  
Vortex Patterns

Microbioreactors are gaining increased interest in biopharmaceutical research. Due to their decreasing size, the parallelization of multiple reactors allows for simultaneous experiments. This enables the generation of high amounts of valuable data with minimal consumption of precious pharmaceutical substances. However, in bioreactors of all scales, fast mixing represents a crucial condition. Efficient transportation of nutrients to the cells ensures good growing conditions, homogeneous environmental conditions for all cultivated cells, and therefore reproducible and valid data. For these reasons, a new type of batch microbioreactor was developed in which any moving mixer component is rendered obsolete through the utilization of capillary surface waves for homogenization. The bioreactor was fabricated in photosensitive glass and its fluid volume of up to 8 µL was provided within a bowl-shaped volume. External mechanical actuators excited capillary surface waves and stereo microparticle image velocimetry (µPIV) was used to analyze resulting convection at different excitation conditions in varied reactor geometries. Typical vortex patterns were observed at certain resonance frequencies where best mixing conditions occurred. Based on the results, a simplified 1D model which predicts resonance frequencies was evaluated. Cultivation of Escherichia coli BL21 under various mixing conditions showed that mixing in resonance increased the biomass growth rate, led to high biomass concentrations, and provided favorable growth conditions. Since glass slides containing multiple bowl reactors can be excited as a whole, massive parallelization is foreseen.

scholarly journals Large-scale selection synchrony of Tetrahymena thermophila

1986 ◽  
Vol 84 (1) ◽  
pp. 237-251
Author(s):  
R.J. Hill ◽  
T. Kroft ◽  
M. Zuker ◽  
I.C. Smith
Keyword(s):  
Cell Cycle ◽  
Cell Culture ◽  
Cell Population ◽  
Large Scale ◽  
Doubling Time ◽  
Tetrahymena Thermophila ◽  
Growth Conditions ◽  
Scale Selection

A method is described, based on the phagocytosis of colloidal ferrite particles, which gives highly synchronous populations of Tetrahymena thermophila. To ensure a successful synchrony, the cell culture doubling time, the limits of the phagocytic period and the distribution of cell stages must first be determined. Once these parameters are known, synchrony can be achieved under a variety of growth conditions and with cultures ranging in volume from a few millilitres to 12 litres or more. The main advantages of the method are that the apparatus required is simple, large volumes of cells can be handled easily, and the synchronous populations can be prepared within a few hours. In principle, the method should be applicable to any cell population in which phagocytosis occurs discontinuously over the cell cycle.

scholarly journals A model for variable phytoplankton stoichiometry based on cell protein regulation

2013 ◽  
Vol 10 (2) ◽  
pp. 3241-3279
Author(s):  
J. A. Bonachela ◽  
S. D. Allison ◽  
A. C. Martiny ◽  
S. A. Levin
Keyword(s):  
Physiological State ◽  
Single Point ◽  
Nutrient Content ◽  
Growth Conditions ◽  
Marine Phytoplankton ◽  
Cell Protein ◽  
Nitrogen And Phosphorus ◽  
Elemental Ratios ◽  
Regulatory Processes ◽  
Complex Interactions

Abstract. The elemental ratios of marine phytoplankton emerge from complex interactions between the biotic and abiotic components of the ocean, and reflect the plastic response of individuals to changes in their environment. The stoichiometry of phytoplankton is, thus, dynamic and dependent on the physiological state of the cell. We present a theoretical model for the dynamics of the carbon, nitrogen and phosphorus contents of a phytoplankton population. By representing the regulatory processes controlling nutrient uptake, and focusing on the relation between nutrient content and protein synthesis, our model qualitatively replicates existing experimental observations for nutrient content and ratios. The population described by our model takes up nutrients in proportions that match the input ratios for a broad range of growth conditions. In addition, there are two zones of single-nutrient limitation separated by a wide zone of co-limitation. Within the co-limitation zone, a single point can be identified where nutrients are supplied in an optimal ratio. The existence of a wide co-limitation zone affects the standard picture for species competing for nitrogen and phosphorus, which shows here a much richer pattern. However, additional comprehensive laboratory experiments are needed to test our predictions. Our model contributes to the understanding of the global cycles of oceanic nitrogen and phosphorus, as well as the elemental ratios of these nutrients in phytoplankton populations.

scholarly journals Chromosomal Rearrangements in Salmonella enterica Serovar Typhi Strains Isolated from Asymptomatic Human Carriers

mBio ◽  
2011 ◽  
Vol 2 (3) ◽  
Author(s):  
T. David Matthews ◽  
Wolfgang Rabsch ◽  
Stanley Maloy
Keyword(s):  
Salmonella Enterica ◽  
Large Scale ◽  
Chromosomal Rearrangements ◽  
Growth Conditions ◽  
Genetic Changes ◽  
Content Type ◽  
Long Term Storage ◽  
Bacterial Chromosomes ◽  
Over Time

ABSTRACTHost-specific serovars ofSalmonella entericaoften have large-scale chromosomal rearrangements that occur by recombination betweenrrnoperons. Two hypotheses have been proposed to explain these rearrangements: (i) replichore imbalance from horizontal gene transfer drives the rearrangements to restore balance, or (ii) the rearrangements are a consequence of the host-specific lifestyle. Although recent evidence has refuted the replichore balance hypothesis, there has been no direct evidence for the lifestyle hypothesis. To test this hypothesis, we determined therrnarrangement type for 20Salmonella entericaserovar Typhi strains obtained from human carriers at periodic intervals over multiple years. These strains were also phage typed and analyzed for rearrangements that occurred over long-term storage versus routine culturing. Strains isolated from the same carrier at different time points often exhibited different arrangement types. Furthermore, colonies isolated directly from the Dorset egg slants used to store the strains also had different arrangement types. In contrast, colonies that were repeatedly cultured always had the same arrangement type. Estimated replichore balance of isolated strains did not improve over time, and some of the rearrangements resulted in decreased replicore balance. Our results support the hypothesis that the restricted lifestyle of host-specificSalmonellais responsible for the frequent chromosomal rearrangements in these serovars.IMPORTANCEAlthough it was previously thought that bacterial chromosomes were stable, comparative genomics has demonstrated that bacterial chromosomes are dynamic, undergoing rearrangements that change the order and expression of genes. While mostSalmonellastrains have a conserved chromosomal arrangement type, rearrangements are very common in host-specificSalmonellastrains. This study suggests that chromosome rearrangements in the host-specificSalmonella entericaserovar Typhi, the causal agent of typhoid fever, occur within the human host over time. The results also indicate that rearrangements can occur during long-term maintenance on laboratory medium. Although these genetic changes do not limit survival under slow-growth conditions, they may limit the survival ofSalmonellaTyphi in other environments, as predicted for the role of pseudogenes and genome reduction in niche-restricted bacteria.

scholarly journals A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Nelly F Mostajo ◽  
Marie Lataretu ◽  
Sebastian Krautwurst ◽  
Florian Mock ◽  
Daniel Desirò ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Large Scale ◽  
Viral Infections ◽  
Gene Expression Regulation ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Regulatory Processes ◽  
Genome Annotations ◽  
Host Virus Interactions

Abstract Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.

scholarly journals Role of the Streptococcus mutans irvA Gene in GbpC-Independent, Dextran-Dependent Aggregation and Biofilm Formation

2009 ◽  
Vol 75 (22) ◽  
pp. 7037-7043 ◽  
Author(s):  
Min Zhu ◽  
Dragana Ajdić ◽  
Yuan Liu ◽  
David Lynch ◽  
Justin Merritt ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Biofilm Formation ◽  
Growth Conditions ◽  
Parental Background ◽  
A Cell ◽  
Major Surface ◽  
Biofilm Development ◽  
Small Aggregation

ABSTRACT Dextran-dependent aggregation (DDAG) of Streptococcus mutans is an in vitro phenomenon that is believed to represent a property of the organism that is beneficial for sucrose-dependent biofilm development. GbpC, a cell surface glucan-binding protein, is responsible for DDAG in S. mutans when cultured under defined stressful conditions. Recent reports have described a putative transcriptional regulator gene, irvA, located just upstream of gbpC, that is normally repressed by the product of an adjacent gene, irvR. When repression of irvA is relieved, there is a resulting increase in the expression of GbpC and decreases in competence and synthesis of the antibiotic mutacin I. This study examined the role of irvA in DDAG and biofilm formation by engineering strains that overexpressed irvA (IrvA+) on an extrachromosomal plasmid. The IrvA+ strain displayed large aggregation particles that did not require stressful growth conditions. A novel finding was that overexpression of irvA in a gbpC mutant background retained a measure of DDAG, albeit very small aggregation particles. Biofilms formed by the IrvA+ strain in the parental background possessed larger-than-normal microcolonies. In a gbpC mutant background, the overexpression of irvA reversed the fragile biofilm phenotype normally associated with loss of GbpC. Real-time PCR and Northern blot analyses found that expression of gbpC did not change significantly in the IrvA+ strain but expression of spaP, encoding the major surface adhesin P1, increased significantly. Inactivation of spaP eliminated the small-particle DDAG. The results suggest that IrvA promotes DDAG not only by GbpC, but also via an increase in P1.

scholarly journals Peptidergic control of food intake and digestion in insects 1This review is part of a virtual symposium on recent advances in understanding a variety of complex regulatory processes in insect physiology and endocrinology, including development, metabolism, cold hardiness, food intake and digestion, and diuresis, through the use of omics technologies in the postgenomic era.

2012 ◽  
Vol 90 (4) ◽  
pp. 489-506 ◽  
Author(s):  
J. Spit ◽  
L. Badisco ◽  
H. Verlinden ◽  
P. Van Wielendaele ◽  
S. Zels ◽  
...  
Keyword(s):  
Food Intake ◽  
Cold Hardiness ◽  
Endocrine Cells ◽  
Large Scale ◽  
Regulatory Peptides ◽  
Regulatory Processes ◽  
Peptide Precursor ◽  
Multiple Levels ◽  
Physiological Tasks ◽  
Saliva Production

Like all heterotrophic organisms, insects require a strict control of food intake and efficient digestion of food into nutrients to maintain homeostasis and to fulfill physiological tasks. Feeding and digestion are steered by both external and internal signals that are transduced by a multitude of regulatory factors, delivered either by neurons innervating the gut or mouthparts, or by midgut endocrine cells. The present review gives an overview of peptide regulators known to control feeding and digestion in insects. We describe the discovery and functional role in these processes for insect allatoregulatory peptides, diuretic hormones, FMRFamide-related peptides, (short) neuropeptide F, proctolin, saliva production stimulating peptides, kinins, and tachykinins. These peptides control either gut myoactivity, food intake, and (or) release of digestive enzymes. Some peptides exert their action at multiple levels, possibly having a biological function that depends on their site of delivery. Many regulatory peptides have been physically extracted from different insect species. However, multiple peptidomics, proteomics, transcriptomics, and genome sequencing projects have led to increased discovery and prediction of peptide (precursor) and receptor sequences. In combination with physiological experiments, these large-scale projects have already led to important steps forward in unraveling the physiology of feeding and digestion in insects.

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