A Graph Theory Approach for Regional Controllability of Boolean Cellular Automata

Controllability is one of the central concepts of modern control theory that allows a good understanding of a system's behaviour. It consists in constraining a system to reach the desired state from an initial state within a given time interval. When the desired objective affects only a sub-region of the domain, the control is said to be regional. The purpose of this paper is to study a particular case of regional control using cellular automata models since they are spatially extended systems where spatial properties can be easily defined thanks to their intrinsic locality. We investigate the case of boundary controls on the target region using an original approach based on graph theory. Necessary and sufficient conditions are given based on the Hamiltonian Circuit and strongly connected component. The controls are obtained using a preimage approach

Effect of Cyclic Heat Stress on Feeding-Related Hypothalamic Neuropeptides of Three Broiler Populations and Their Ancestor Jungle Fowl

open6siThis study was supported by a grant from the Arkansas Division of Agriculture, Animal Health Awards (to SD and SO) and from USDA-AFRI Sustainable Agriculture Systems (2019-69012-29905) to SD.Heat stress (HS) has been increasingly jeopardizing the sustainability of the poultry production. Moreover, modern high-performing chickens are far less able to withstand HS than their predecessors due to higher growth rate and metabolic rates. Performance losses caused by HS are mainly ascribed to decreases in feed consumption. Since feed intake is tightly controlled by the hypothalamic centers of hunger and satiety, we sought to determine the effect of chronic cyclic HS on the expression of feedingrelated hypothalamic neuropeptides (FRHN) in unselected chickens (i.e., the ancestor junglefowl—JF) and three broiler lines from diverse stages of genetic selection (i.e., the slow growing ACRB, the moderate growing 95RN, and the fast growing MRB). From 29 to 56 days, birds (n = 150 birds for each population) were subjected to either thermoneutral (TN, 25C) or cyclic heat stress (HS, 36C, 0900–1,800 h) conditions. Molecular data were analyzed by two-way ANOVA with interaction between the main factors, namely environmental temperature and line. The expression of major FHRN, like neuropeptide Y, agouti-related peptide, proopiomelanocortin, and cocaine and amphetamine regulated transcript remained unchanged. However, melanocortin receptor 1 exhibited a line-dependent decreasing trend from JF to MRB under both TN and HS (p = 0.09), adiponectin expression showed a distinct trend toward significance with 95RB exhibiting the highest mRNA level irrespective of the environmental temperature (p = 0.08), and JF had a greater mRNA abundance of visfatin than ACRB under TN (p < 0.05). The hypothalamic integration of circadian information, acclimation to long-lasting HS exposure, stable ypothalamic pathways unaffected by evolution and genetic selection, focus on mRNA abundances, and use of the entire hypothalamus masking gene expression in specific hypothalamic nuclei are all possible explanations for the lack of variations observed in this study. In conclusion, this is the first assessment of the impacts of heat stress on feeding-related hypothalamic neuropeptides of chicken, with a valuable and informative comparison between the ancestor junglefowl and three differently performing broiler lines.openGiorgio Brugaletta, Elizabeth Greene, Travis Tabler, Sara Orlowski, Federico Sirri, Sami DridiGiorgio Brugaletta, Elizabeth Greene, Travis Tabler, Sara Orlowski, Federico Sirri, Sami Drid

Effect of Cyclic Heat Stress on Hypothalamic Oxygen Homeostasis and Inflammatory State in the Jungle Fowl and Three Broiler-Based Research Lines

Heat stress (HS) is devastating to poultry production sustainability due its detrimental effects on performance, welfare, meat quality, and profitability. One of the most known negative effects of HS is feed intake depression, which is more pronounced in modern high-performing broilers compared to their ancestor unselected birds, yet the underlying molecular mechanisms are not fully defined. The present study aimed, therefore, to determine the hypothalamic expression of a newly involved pathway, hypoxia/oxygen homeostasis, in heat-stressed broiler-based research lines and jungle fowl. Three populations of broilers (slow growing ACRB developed in 1956, moderate growing 95RB from broilers available in 1995, and modern fast growing MRB from 2015) and unselected Jungle fowl birds were exposed to cyclic heat stress (36 degrees C, 9 h/day for 4 weeks) in a 2 x 4 factorial experimental design. Total RNAs and proteins were extracted from the hypothalamic tissues and the expression of target genes and proteins was determined by real-time quantitative PCR and Western blot, respectively. It has been previously shown that HS increased core body temperature and decreased feed intake in 95RB and MRB, but not in ACRB or JF. HS exposure did not affect the hypothalamic expression of HIF complex, however there was a line effect for HIF-1 alpha (P = 0.02) with higher expression in JF under heat stress. HS significantly up regulated the hypothalamic expression of hemoglobin subunits (HBA1, HBBR, HBE, HBZ), and HJV in ACRB, HBA1 and HJV in 95RB and MRB, and HJV in JF, but it down regulated FPN1 in JF. Additionally, HS altered the hypothalamic expression of oxygen homeostasis- up and down-stream signaling cascades. Phospho-AMPK(Thr172) was activated by HS in JF hypothalamus, but it decreased in that of the broiler-based research lines. Under thermoneutral conditions, p-AMPK(Thr172) was higher in broiler-based research lines compared to JF. Ribosomal protein S6K1, however, was significantly upregulated in 95RB and MRB under both environmental conditions. HS significantly upregulated the hypothalamic expression of NF-kappa B2 in MRB, RelB, and TNF alpha in ACRB, abut it down regulated RelA in 95RB. The regulation of HSPs by HS seems to be family- and line-dependent. HS upregulated the hypothalamic expression of HSP60 in ACRB and 95RB, down regulated HSP90 in JF only, and decreased HSP70 in all studied lines. Taken together, this is the first report showing that HS modulated the hypothalamic expression of hypoxia- and oxygen homeostasis-associated genes as well as their up- and down-stream mediators in chickens, and suggests that hypoxia, thermotolerance, and feed intake are interconnected, which merit further in-depth investigations

Effects of Cyclic Chronic Heat Stress on the Expression of Nutrient Transporters in the Jejunum of Modern Broilers and Their Ancestor Wild Jungle Fowl

snibaThe mechanisms associated between growth rate, gut integrity and heat stress (HS) responses are not known. The current study aimed to evaluate the effect of chronic HS on jejunal nutrient transport in slow- (ACRB from 1950), moderate- (95RAN from 1995), rapid-(modern broilers, MRB) growing birds, and their ancestor wild jungle fowl (JF). One-day male chicks (n=150/line) were placed by line in environmentally controlled chambers and kept under the same environmental conditions until d28. On d29, an 8-h daily cyclic HS (36ºC) was applied to half of the chambers, which lasts until d55, while keeping the rest under thermal neutral conditions (TN, 24°C). Jejunum tissues were collected for morphology assessment and molecular analysis of carbohydrate-, amino acid- and fatty acid- transporters. MRB exhibited the highest BW followed by 95RAN under both conditions. HS decreased FI in MRB and 95RAN, which results in lower BW compared to their TN counterparts, however no effect was observed in ACRB and JF. MRB showed greater villus height to crypt depth ratio under both environmental conditions. Molecular analyses showed that GLUT2, 5, 10, and 11 were upregulated in MRB compared to some of the other populations under TN conditions. HS down regulated GLUT2, 10, 11, and 12 in MRB while it increased the expression of GLUT1, 5, 10, and 11 in JF. GLUT2 protein expression was higher in JF compared to ACRB and MRB under TN conditions. It also showed an increase in ACRB but no effect on 95RAN and MRB under HS conditions. ACRB exhibited greater expression of EAAT3 gene as compared to the rest of populations maintained under TN conditions. HS exposure did not alter the gene expression of amino acid transporters in MRB. Gene expression of CD36 and FABP2 was up-regulated in HS JF birds. Protein expression of CD36 was down-regulated in HS JF while no effect was observed in ACRB, 95RAN and MRB. Taken together, these data are the first to show the effect of HS on jejunal expression of nutrient transporters in three broiler populations known to represent 70 years of genetic progress in the poultry industr

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Nouvelles avancées en contrôlabilité régionale des automates cellulaires

The issue addressed in this thesis concerns the controllability of a class of discrete spatio-temporal systems named cellular automata (CA). The purpose of this study is to highlight new ways to prove the controllability of complex systems. Morespecifically, this thesis focuses on regional controllability which consists in restricting the study to a subregion of the domain where the system will have to achieve a given objective through targeted actions. The case of Boolean CA have been particularly examined throughout this thesis. The first part is devoted to the study of the problem of the regional controllability of deterministic CAs when the actions are exerted on the boundaries of the controlled region. A first approach that we used relies on Markov chains and controllability is characterized by establishing a matrix similar to their transition matrix using the definitions of a regular and ergodic chain. This study has been extended to the case of probabilistic CAs that are widely used tomodel many real phenomena. The same problem has been apprehended using tools of graph theory. We proposenecessary and sufficient conditions for the regional controllability of deterministic CAs using the notions of Hamiltonian circuit and strongly connected component. The control that ensures regional controllability is defined through a preimage algorithm.The second part is devoted to the problem of the boundary regional controllability of Boolean CAs, which consists of acting on the boundary of the domain in order to reach a desired goal in a target region. We first consider linear CAs for which we givea characterization result using the Kalman condition. We propose an algorithm to determine the control that allows to force the appearance of a desired configuration in the study area. The case of nonlinear CAs was also considered using a preimagesearch algorithm.Le sujet abordé dans cette thèse concerne la contrôlabilité d’une classe de systèmes spatio-temporels, entièrement discrets de type automates cellulaires (AC). Le but de cette étude est de mettre en lumière de nouvelles pistes pour prouver la contrôlabilité des systèmes complexes. Plus spécifiquement, cette thèse se focalise sur la contrôlabilité régionale qui consiste à se restreindre à une région du domaine où le système devra atteindre un objectif donné à travers des actions ciblées. Le cas d’AC Booléens a été particulièrement examiné tout au long de cette thèse. La première partie est consacrée à l’étude du problème de la contrôlabilité régionale des AC déterministes lorsque les actions sont exercées sur la frontière de la régioncontrôlée. Une première démarche que nous avons utilisée s’appuie sur les chaines de Markov et la contrôlabilité est caractérisée en établissant une matrice similaire à leur matrice de transition en utilisant les définitions d’une chaîne ergodique et régulière. Cette étude a été étendue au cas des AC probabilistes qui sont largement utilisés pour modéliser de nombreux phénomènes réels. Le même problème a été appréhendé en utilisant des outils de la théorie des graphes. Nous proposons des conditions nécessaires et suffisantes pour la contrôlabilité régionale des AC déterministes en utilisant les notions de circuit hamiltonien et de composante fortement connexe. Le contrôle qui assure la contrôlabilité régionale est défini à travers un algorithme préimages. La deuxième partie est dédiée au problème de la contrôlabilité régionale frontière des AC Booléens qui consiste à agir sur la frontière du domaine pour atteindre un objectif sur une région cible. Nous considérons d’abord des AC linéaires pour lesquels nousdonnons un résultat de caractérisation grâce à la condition de Kalman. Nous proposons un algorithme pour déterminer le contrôle qui permet de forcer l’apparition d’une configuration désirée dans la région d’étude. Le cas des AC non linéaires a été également considéré en utilisant un algorithme de recherche des préimages

Markov Chains Approach for Regional Controllability of Deterministic Cellular Automata, via Boundary Actions

International audienceThis paper is focused on studying the problem of regional controllability via boundary actions on a target region of a deterministic Cellular Automaton (CA). This problem has already been studied for continuous systems described by partial differential equations (PDEs). The concept of controllability was first identified by R. Kalman in 1960. In linear systems analysis, the Kalman rank condition is omnipresent and was used to obtain the main characterization results on controllability. The purpose of this paper is to study this concept applied to Cellular Automata models considered as the discrete counterpart of PDEs. We focus on regional controllability that considers objectives to be achieved only on a subregion of the whole domain and the controls exerted on the boundary of the target region. We prove the regional controllability of two dimensional deterministic linear cellular automata by exploring a new approach based on Markov chains. The extension to non-linear CA has also been studied

Markov Chains Approach for Regional Controllability of Deterministic Cellular Automata, via Boundary Actions

International audienceThis paper is focused on studying the problem of regional controllability via boundary actions on a target region of a deterministic Cellular Automaton (CA). This problem has already been studied for continuous systems described by partial differential equations (PDEs). The concept of controllability was first identified by R. Kalman in 1960. In linear systems analysis, the Kalman rank condition is omnipresent and was used to obtain the main characterization results on controllability. The purpose of this paper is to study this concept applied to Cellular Automata models considered as the discrete counterpart of PDEs. We focus on regional controllability that considers objectives to be achieved only on a subregion of the whole domain and the controls exerted on the boundary of the target region. We prove the regional controllability of two dimensional deterministic linear cellular automata by exploring a new approach based on Markov chains. The extension to non-linear CA has also been studied