Maiasaura, a model organism for extinct vertebrate population biology: a large sample statistical assessment of growth dynamics and survivorship (project)

AbstractFossil bone microanalyses reveal the ontogenetic histories of extinct tetrapods, but incomplete fossil records often result in small sample sets lacking statistical strength. In contrast, a histological sample of 50 tibiae of the hadrosaurid dinosaurMaiasaura peeblesorumallows predictions of annual growth and ecological interpretations based on more histologic data than any previous large sample study. Tibia length correlates well (R2>0.9) with diaphyseal circumference, cortical area, and bone wall thickness, thereby allowing longitudinal predictions of annual body size increases based on growth mark circumference measurements. With an avian level apposition rate of 86.4 μm/day,Maiasauraachieved over half of asymptotic tibia diaphyseal circumference within its first year. Mortality rate for the first year was 89.9% but a seven year period of peak performance followed, when survivorship (mean mortality rate=12.7%) was highest. During the third year of life,Maiasauraattained 36% (x=1260 kg) of asymptotic body mass, growth rate was decelerating (18.2 μm/day), cortical vascular orientation changed, and mortality rate briefly increased. These transitions may indicate onset of sexual maturity and corresponding reallocation of resources to reproduction. Skeletal maturity and senescence occurred after 8 years, at which point the mean mortality rate increased to 44.4%. Compared withAlligator, an extant relative,Maiasauraexhibits rapid cortical increase early in ontogeny, whileAlligatorcortical growth is much lower and protracted throughout ontogeny. Our life history synthesis ofMaiasaurautilizes the largest histological sample size for any extinct tetrapod species thus far, demonstrating how large sample microanalyses strengthen paleobiological interpretations.

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Dynamics of Consumer-Resource Systems

Population and Community Ecology of Ontogenetic Development ◽

10.23943/princeton/9780691137575.003.0009 ◽

2013 ◽

Author(s):

André M. de Roos ◽

Lennart Persson

Keyword(s):

Model Organism ◽

Growth Dynamics ◽

Population Cycles ◽

Food Density ◽

Juvenile Period ◽

Ecological Processes ◽

Resource Dynamics ◽

Cladoceran Zooplankton ◽

The Individual ◽

Consumer Resource

This chapter focuses on consumer-resource dynamics in systems where consumers of different sizes compete for a shared resource. It considers the implications of three important aspects of consumer life history: the explicit handling of a juvenile period leading to a delay between the time when an individual is born to when it starts to reproduce; the rate by which individual ecological processes scale with body size; and whether the rate by which the individual grows is dependent on food density or not. The chapter examines the effects of different resource growth dynamics to illustrate the fundamental differences between population cycles driven by interactions between individuals of different sizes, and classical predator–prey cycles driven by interactions between the consumer and the resource, also referred to as paradox of enrichment cycles. It also discusses experiments with the model organism, the cladoceran zooplankton Daphnia, to elucidate our current understanding of cycles driven by cohort interactions in this organism.

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Length regulation of multiple flagella that self-assemble from a shared pool of components

10.1101/436360 ◽

2018 ◽

Cited By ~ 2

Author(s):

Thomas G. Fai ◽

Lishibanya Mohapatra ◽

Jane Kondev ◽

Ariel Amir

Keyword(s):

Chlamydomonas Reinhardtii ◽

Inverse Relationship ◽

Model Organism ◽

Growth Dynamics ◽

Size Control ◽

Control Model ◽

Mass Action ◽

Law Of Mass Action ◽

Length Regulation ◽

Coupling Mechanisms

AbstractControl of organelle size is a problem that has intrigued cell biologists for at least a century. The single-celled green algaeChlamydomonas reinhardtiiwith its two 2agella has proved to be a very useful model organism for studies of size control. Numerous experiments have identi1ed motor-driven transport of tubulin to the growing ends of microtubules at the tip of the 2agella as the key component of the machinery responsible for controlling their length. Here we consider a model of 2agellar length control whose key assumption is that proteins responsible for the intra2agellar transport (IFT) of tubulin are present in limiting amounts. We show that this limiting-pool assumption and simple reasoning based on the law of mass action leads to an inverse relationship between the rate at which a 2agellum grows and its length, which has been observed experimentally, and has been shown theoretically to provide a mechanism for length control. Experiments in which one of the two 2agella are severed have revealed the coupled nature of the growth dynamics of the two 2agella, and we extend our length-control model to two 2agella by considering different mechanisms of their coupling. We describe which coupling mechanisms are capable of reproducing the observed dynamics in severing experiments, and why some that have been proposed previously are not. Within our theoretical framework we conclude that if tubulin and IFT proteins are freely exchanged between 2agella simultaneous length control is not possible if the disassembly rate is constant. However, if disassembly depends on the concentration of IFT proteins at the tip of the 2agellum, simultaneous length control can be achieved. Finally, we make quantitative predictions for experiments that could test this model.

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Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors

10.1101/2021.07.22.453334 ◽

2021 ◽

Author(s):

Sara Moreno-Paz ◽

Joep Schmitz ◽

Vitor A.P. Martins dos Santos ◽

Maria Suarez-Diez

Keyword(s):

Saccharomyces Cerevisiae ◽

Model Organism ◽

Growth Dynamics ◽

Operational Conditions ◽

Strain Design ◽

Balance Analysis ◽

Different Strains ◽

Batch Bioreactors ◽

Constrained Models ◽

Genome Scale

Genome-scale, constraint-based models (GEM) and their derivatives are commonly used to model and gain insights into microbial metabolism. Often, however, their accuracy and predictive power are limited and enable only approximate designs. To improve their usefulness for strain and bio-process design, we studied here their capacity to accurately predict metabolic changes in response to operational conditions in a bioreactor, as well as intracellular, active reactions. We used flux balance analysis (FBA) and dynamic FBA (dFBA) to predict growth dynamics of the model organism Saccharomyces cerevisiae under different industrially relevant conditions. We compared simulations with the latest developed GEM for this organism (Yeast8) and its enzyme-constrained version (ecYeast8) herein described with experimental data and found that ecYeast8 outperforms Yeast8 in all the simulations. EcYeast8 was able to predict well-known traits of yeast metabolism including the onset of the Crabtree effect, the order of substrate consumption during mixed carbon cultivation and production of a target metabolite. We showed how the combination of ecGEM and dFBA links reactor operation and genetic modifications to flux predictions, enabling the prediction of yields and productivities of different strains and (dynamic) production processes. Additionally, we present flux sampling as a tool to analyze flux predictions of ecGEM, of major importance for strain design applications. We showed that constraining protein availability substantially improves accuracy of the description of the metabolic state of the cell under dynamic conditions. This therefore enables more realistic and faithful designs of industrially relevant cell-based processes and, thus, the usefulness of such models

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Growth Dynamics and Survival of Liberibacter crescens BT-1, an Important Model Organism for the Citrus Huanglongbing Pathogen “Candidatus Liberibacter asiaticus”

Applied and Environmental Microbiology ◽

10.1128/aem.01656-19 ◽

2019 ◽

Vol 85 (21) ◽

Cited By ~ 2

Author(s):

Marta Sena-Vélez ◽

Sean D. Holland ◽

Manu Aggarwal ◽

Nick G. Cogan ◽

Mukesh Jain ◽

...

Keyword(s):

Plant Pathogens ◽

Genetic Manipulation ◽

Model Organism ◽

Growth Dynamics ◽

Culture Conditions ◽

Citrus Greening ◽

Close Relative ◽

Logarithmic Phase ◽

Content Type ◽

Liberibacter Asiaticus

ABSTRACT Liberibacter crescens is the only cultured member of its genus, which includes the devastating plant pathogen “Candidatus Liberibacter asiaticus,” associated with citrus greening/Huanglongbing (HLB). L. crescens has a larger genome and greater metabolic flexibility than “Ca. Liberibacter asiaticus” and the other uncultured plant-pathogenic Liberibacter species, and it is currently the best model organism available for these pathogens. L. crescens grows slowly and dies rapidly under current culture protocols and this extreme fastidiousness makes it challenging to study. We have determined that a major cause of rapid death of L. crescens in batch culture is its alkalinization of the medium (to pH 8.5 by the end of logarithmic phase). The majority of this alkalinization is due to consumption of alpha-ketoglutaric acid as its primary carbon source, with a smaller proportion of the pH rise due to NH3 production. Controlling the pH rise with higher buffering capacity and lower starting pH improved recoverability of cells from 10-day cultures by >1,000-fold. We have also performed a detailed analysis of L. crescens growth with total cell numbers calibrated to the optical density and the percentage of live and recoverable bacteria determined over 10-day time courses. We modified L. crescens culture conditions to greatly enhance survival and increase maximum culture density. The similarities between L. crescens and the pathogenic liberibacters make this work relevant to efforts to culture the latter organisms. Our results also suggest that growth-dependent pH alteration that overcomes medium buffering should always be considered when growing fastidious bacteria. IMPORTANCE Liberibacter crescens is a bacterium that is closely related to plant pathogens that have caused billions of dollars in crop losses in recent years. Particularly devastating are citrus losses due to citrus greening disease, also known as Huanglongbing, which is caused by “Candidatus Liberibacter asiaticus” and carried by the Asian citrus psyllid. L. crescens is the only close relative of “Ca. Liberibacter asiaticus” that can currently be grown in culture, and it therefore serves as an important model organism for the growth, genetic manipulation, and biological control of the pathogenic species. Here, we show that one of the greatest limitations to L. crescens growth is the sharp increase in alkaline conditions it produces as a consequence of consumption of its preferred nutrient source. In addition to new information about L. crescens growth and metabolism, we provide new guidelines for culture conditions that improve the survival and yield of L. crescens.

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Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab213 ◽

2021 ◽

Author(s):

Jeffrey M Skerker ◽

Kaila M Pianalto ◽

Stephen J Mondo ◽

Kunlong Yang ◽

Adam P Arkin ◽

...

Keyword(s):

Aspergillus Flavus ◽

Population Biology ◽

Draft Genome ◽

Model Organism ◽

Opportunistic Pathogen ◽

Protein Coding ◽

Oxford Nanopore ◽

Long Read ◽

New Gene ◽

Major Producer

Abstract Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.

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Cristal-growth dynamics of n-doped gaAs

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100132352 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1544-1545

Author(s):

Pham V. Huong ◽

Stéphanie Bouchet ◽

Jean-Claude Launay

Keyword(s):

Crystal Growth ◽

Spatial Resolution ◽

Epitaxial Layer ◽

Outer Surface ◽

Gaas Substrate ◽

Structural Modification ◽

Growth Dynamics ◽

Argon Laser ◽

High Anisotropy ◽

Crystal Gaas

Microstructure of epitaxial layers of doped GaAs and its crystal growth dynamics on single crystal GaAs substrate were studied by Raman microspectroscopy with a Dilor OMARS instrument equipped with a 1024 photodiode multichannel detector and a ion-argon laser Spectra-Physics emitting at 514.5 nm.The spatial resolution of this technique, less than 1 μm2, allows the recording of Raman spectra at several spots in function of thickness, from the substrate to the outer deposit, including areas around the interface (Fig.l).The high anisotropy of the LO and TO Raman bands is indicative of the orientation of the epitaxial layer as well as of the structural modification in the deposit and in the substrate at the interface.With Sn doped, the epitaxial layer also presents plasmon in Raman scattering. This fact is already very well known, but we additionally observed that its frequency increases with the thickness of the deposit. For a sample with electron density 1020 cm-3, the plasmon L+ appears at 930 and 790 cm-1 near the outer surface.

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