Resource allocation in living organisms

2017 ◽  
Vol 45 (4) ◽  
pp. 945-952 ◽  
Author(s):  
Anne Goelzer ◽  
Vincent Fromion
Keyword(s):  
Resource Allocation ◽  
Quantitative Prediction ◽  
Cellular Models ◽  
Wide Range ◽  
Balance Analysis ◽  
Good Trade ◽  
Living Organisms ◽  
Individual Scale ◽  
The Individual ◽  
Genome Scale

Quantitative prediction of resource allocation for living systems has been an intensive area of research in the field of biology. Resource allocation was initially investigated in higher organisms by using empirical mathematical models based on mass distribution. A challenge is now to go a step further by reconciling the cellular scale to the individual scale. In the present paper, we review the foundations of modelling of resource allocation, particularly at the cellular scale: from small macro-molecular models to genome-scale cellular models. We enlighten how the combination of omic measurements and computational advances together with systems biology has contributed to dramatic progresses in the current understanding and prediction of cellular resource allocation. Accurate genome-wide predictive methods of resource allocation based on the resource balance analysis (RBA) framework have been developed and ensure a good trade-off between the complexity/tractability and the prediction capability of the model. The RBA framework shows promise for a wide range of applications in metabolic engineering and synthetic biology, and for pursuing investigations of the design principles of cellular and multi-cellular organisms.

scholarly journals A data-driven method for reconstructing and modelling social interactions in moving animal groups

2020 ◽  
Vol 375 (1807) ◽  
pp. 20190380 ◽  
Author(s):  
R. Escobedo ◽  
V. Lecheval ◽  
V. Papaspyros ◽  
F. Bonnet ◽  
F. Mondada ◽  
...  
Keyword(s):  
Social Interactions ◽  
Social Systems ◽  
Quantitative Description ◽  
Group Living ◽  
Quantitative Model ◽  
Individual Level ◽  
Wide Range ◽  
Living Organisms ◽  
Individual Scale ◽  
The Individual

Group-living organisms that collectively migrate range from cells and bacteria to human crowds, and include swarms of insects, schools of fish, and flocks of birds or ungulates. Unveiling the behavioural and cognitive mechanisms by which these groups coordinate their movements is a challenging task. These mechanisms take place at the individual scale and can be described as a combination of interactions between individuals and interactions between these individuals and the physical obstacles in the environment. Thanks to the development of novel tracking techniques that provide large and accurate datasets, the main characteristics of individual and collective behavioural patterns can be quantified with an unprecedented level of precision. However, in a large number of studies, social interactions are usually described by force map methods that only have a limited capacity of explanation and prediction, being rarely suitable for a direct implementation in a concise and explicit mathematical model. Here, we present a general method to extract the interactions between individuals that are involved in the coordination of collective movements in groups of organisms. We then apply this method to characterize social interactions in two species of shoaling fish, the rummy-nose tetra ( Hemigrammus rhodostomus ) and the zebrafish ( Danio rerio ), which both present a burst-and-coast motion. From the detailed quantitative description of individual-level interactions, it is thus possible to develop a quantitative model of the emergent dynamics observed at the group level, whose predictions can be checked against experimental results. This method can be applied to a wide range of biological and social systems. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.

scholarly journals A data-driven method for reconstructing and modelling social interactions in moving animal groups

2019 ◽  
Author(s):  
R. Escobedo ◽  
V. Lecheval ◽  
V. Papaspyros ◽  
F. Bonnet ◽  
F. Mondada ◽  
...  
Keyword(s):  
Social Interactions ◽  
Social Systems ◽  
Quantitative Description ◽  
Group Living ◽  
Data Sets ◽  
Individual Level ◽  
Wide Range ◽  
Living Organisms ◽  
Individual Scale ◽  
The Individual

AbstractGroup-living organisms that collectively migrate range from cells and bacteria to human crowds, and include swarms of insects, schools of fish and flocks of birds or ungulates. Unveiling the behavioural and cognitive mechanisms by which these groups coordinate their movements is a challenging task. These mechanisms take place at the individual scale and they can be described as a combination of pairwise interactions between individuals and interactions between these individuals and the physical obstacles in the environment. Thanks to the development of novel tracking techniques that provide large and accurate data sets, the main characteristics of individual and collective behavioural patterns can be quantified with an unprecedented level of precision. However, in a large number of works, social interactions are usually described by force map methods that only have a limited capacity of explanation and prediction, being rarely suitable for a direct implementation in a concise and explicit mathematical model. Here, we present a general method to extract the interactions between individuals that are involved in the coordination of collective movements in groups of organisms. We then apply this method to characterize social interactions in two species of shoaling fish, the rummynose tetra (Hemigrammus rhodostomus) and the zebrafish (Danio rerio), which both present a burst-and-coast motion. The detailed quantitative description of microscopic individual-level interactions thus provides predictive models of the emergent dynamics observed at the macroscopic group-level. This method can be applied to a wide range of biological and social systems.

Critical assessment of genome-scale metabolic models of Arabidopsis thaliana

2022 ◽  
Author(s):  
Javad Zamani ◽  
Sayed-Amir Marashi ◽  
Tahmineh Lohrasebi ◽  
Mohammad-Ali Malboobi ◽  
Esmail Foroozan
Keyword(s):  
Arabidopsis Thaliana ◽  
Flux Balance Analysis ◽  
Critical Assessment ◽  
Flux Balance ◽  
Balance Analysis ◽  
Metabolic Models ◽  
Living Organisms ◽  
Genome Scale

Genome-scale metabolic models (GSMMs) have enabled researchers to perform systems-level studies of living organisms. As a constraint-based technique, flux balance analysis (FBA) aids computation of reaction fluxes and prediction of...

Reflexion of light by external surfaces of the herring, Clupea harengus

1965 ◽  
Vol 45 (3) ◽  
pp. 711-738 ◽  
Author(s):  
E. J. Denton ◽  
J. A. C. Nicol
Keyword(s):  
Green Light ◽  
Normal Incidence ◽  
Clupea Harengus ◽  
Sea Surface ◽  
Histological Studies ◽  
Fresh Fish ◽  
Wide Range ◽  
Individual Scale ◽  
The Individual

The orientations of the reflecting layers in the external surfaces of the herring have been found both by light-measurements on the fresh fish and by histological studies on preserved specimens.The reflecting platelets which lie under the scales are orientated, with respect to the surface of the fish, in a similar way to the platelets found in the bleak and described earlier by Demon & Nicol (1965). However, on the curved dorsum of the fish, although the reflecting platelets are much more perpendicular to the sea surface than the scales on which they lie, these platelets are still inclined some 20° to the perpendicular. It is shown that, in this region, the fish reflects the fraction of the light striking the platelets which is sufficient to match the background against which the fish is seen. The platelets on the curved dorsum have the property of reflecting green light well if it falls obliquely on them but reflecting it poorly when it strikes them at angles close to normal incidence. On the broad flank of the herring the scales have reflecting platelets under most of their surfaces, and the individual scale has several distinctly coloured regions. When we look at any particular region of the flank of an intact fish we are always looking at several overlapping layers differing greatly from one another in their spectral reflecting properties.It is the combination of the reflexions of several layers which gives the very bright silvery reflexions of the intact fish. A system of overlapping scales of this kind is needed even to reflect one waveband of light well over a wide range of angles of incidence.

scholarly journals Modeling the Differences in Biochemical Capabilities ofPseudomonasSpecies by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Parizad Babaei ◽  
Tahereh Ghasemi-Kahrizsangi ◽  
Sayed-Amir Marashi
Keyword(s):  
In Silico ◽  
Metabolic Networks ◽  
Closely Related Species ◽  
Systematic Analysis ◽  
Reconstruction Process ◽  
Flux Balance ◽  
Wide Range ◽  
Balance Analysis ◽  
Metabolic Models ◽  
Genome Scale

To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. Such models have provided us with a framework for systematic analysis of metabolism. However, little effort has been put towards comparing biochemical capabilities of closely related species using their metabolic models. The accuracy of a model is highly dependent on the reconstruction process, as some errors may be included in the model during reconstruction. In this study, we investigated the ability of threePseudomonasmetabolic models to predict the biochemical differences, namely, iMO1086, iJP962, and iSB1139, which are related toP. aeruginosaPAO1,P. putidaKT2440, andP. fluorescensSBW25, respectively. We did a comprehensive literature search for previous works containing biochemically distinguishable traits over these species. Amongst more than 1700 articles, we chose a subset of them which included experimental results suitable forin silicosimulation. By simulating the conditions provided in the actual biological experiment, we performed case-dependent tests to compare thein silicoresults to the biological ones. We found out that iMO1086 and iJP962 were able to predict the experimental data and were much more accurate than iSB1139.

scholarly journals Challenges and emerging directions in single-cell analysis

2017 ◽  
Author(s):  
Guo-Cheng Yuan ◽  
Long Cai ◽  
Michael Elowitz ◽  
Tariq Enver ◽  
Guoping Fan ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Systematic Investigation ◽  
Cellular Heterogeneity ◽  
Cell Analysis ◽  
Cell Level ◽  
Wide Range ◽  
Molecular Information ◽  
The Individual ◽  
Genome Scale

AbstractSingle-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances, and look to future opportunities.

THE VALUE OF LOVE IN THE SYSTEM OF FORMATION OF THE PROFESSIONAL MATURITY OF THE EDUCATOR

2020 ◽  
Vol 1 (10(79)) ◽  
pp. 12-18
Author(s):  
G. Bubyreva
Keyword(s):  
Russian Federation ◽  
The State ◽  
Educational Process ◽  
Wide Range ◽  
The Family ◽  
The Russian Federation ◽  
The Government ◽  
The Individual ◽  
The Right

The existing legislation determines the education as "an integral and focused process of teaching and upbringing, which represents a socially important value and shall be implemented so as to meet the interests of the individual, the family, the society and the state". However, even in this part, the meaning of the notion ‘socially significant benefit is not specified and allows for a wide range of interpretation [2]. Yet the more inconcrete is the answer to the question – "who and how should determine the interests of the individual, the family and even the state?" The national doctrine of education in the Russian Federation, which determined the goals of teaching and upbringing, the ways to attain them by means of the state policy regulating the field of education, the target achievements of the development of the educational system for the period up to 2025, approved by the Decree of the Government of the Russian Federation of October 4, 2000 #751, was abrogated by the Decree of the Government of the Russian Federation of March 29, 2014 #245 [7]. The new doctrine has not been developed so far. The RAE Academician A.B. Khutorsky believes that the absence of the national doctrine of education presents a threat to national security and a violation of the right of citizens to quality education. Accordingly, the teacher has to solve the problem of achieving the harmony of interests of the individual, the family, the society and the government on their own, which, however, judging by the officially published results, is the task that exceeds the abilities of the participants of the educational process.  The particular concern about the results of the patriotic upbringing served as a basis for the legislative initiative of the RF President V. V. Putin, who introduced the project of an amendment to the Law of RF "About Education of the Russian Federation" to the State Duma in 2020, regarding the quality of patriotic upbringing [3]. Patriotism, considered by the President of RF V. V. Putin as the only possible idea to unite the nation is "THE FEELING OF LOVE OF THE MOTHERLAND" and the readiness for every sacrifice and heroic deed for the sake of the interests of your Motherland. However, the practicing educators experience shortfalls in efficient methodologies of patriotic upbringing, which should let them bring up citizens, loving their Motherland more than themselves. The article is dedicated to solution to this problem based on the Value-sense paradigm of upbringing educational dynasty of the Kurbatovs [15].

Punk as Folk: Continuities and Tensions in the UK and Beyond

2020 ◽  
Author(s):  
Pete Dale
Keyword(s):  
Folk Music ◽  
Music Making ◽  
Collective Creativity ◽  
Living Tradition ◽  
Wide Range ◽  
The Us ◽  
The Common ◽  
The Individual ◽  
The Uk

Numerous claims have been made by a wide range of commentators that punk is somehow “a folk music” of some kind. Doubtless there are several continuities. Indeed, both tend to encourage amateur music-making, both often have affiliations with the Left, and both emerge at least partly from a collective/anti-competitive approach to music-making. However, there are also significant tensions between punk and folk as ideas/ideals and as applied in practice. Most obviously, punk makes claims to a “year zero” creativity (despite inevitably offering re-presentation of at least some existing elements in every instance), whereas folk music is supposed to carry forward a tradition (which, thankfully, is more recognized in recent decades as a subject-to-change “living tradition” than was the case in folk’s more purist periods). Politically, meanwhile, postwar folk has tended more toward a socialist and/or Marxist orientation, both in the US and UK, whereas punk has at least rhetorically claimed to be in favor of “anarchy” (in the UK, in particular). Collective creativity and competitive tendencies also differ between the two (perceived) genre areas. Although the folk scene’s “floor singer” tradition offers a dispersal of expressive opportunity comparable in some ways to the “anyone can do it” idea that gets associated with punk, the creative expectation of the individual within the group differs between the two. Punk has some similarities to folk, then, but there are tensions, too, and these are well worth examining if one is serious about testing out the common claim, in both folk and punk, that “anyone can do it.”

scholarly journals The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants

2021 ◽  
Vol 22 (13) ◽  
pp. 7181
Author(s):  
Seong-Im Park ◽  
Hyeok Jin Kwon ◽  
Mi Hyeon Cho ◽  
Ji Sun Song ◽  
Beom-Gi Kim ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Transcriptional Activation ◽  
Individual Plant ◽  
Hormone Signaling ◽  
Combined Stress ◽  
Drought Treatment ◽  
Wide Range ◽  
The Individual ◽  
Potential Use ◽  
Multiple Stress Tolerance

The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.

scholarly journals Understanding the host-microbe interactions using metabolic modeling

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jack Jansma ◽  
Sahar El Aidy
Keyword(s):  
Human Health ◽  
Flux Balance Analysis ◽  
Bacterial Species ◽  
Flux Balance ◽  
Interaction Field ◽  
In Silico Simulation ◽  
Balance Analysis ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Genome Scale

AbstractThe human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health.

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