Academic literature on the topic 'Spatio-temporal Regulators'

Rho GTPases are crucial signaling molecules that regulate a plethora of biological functions. Traditional biochemical, cell biological, and genetic approaches have founded the basis of Rho GTPase biology. The development of biosensors then allowed measuring Rho GTPase activity with unprecedented spatio-temporal resolution. This revealed that Rho GTPase activity fluctuates on time and length scales of tens of seconds and micrometers, respectively. In this review, we describe Rho GTPase activity patterns observed in different cell systems. We then discuss the growing body of evidence that upstream regulators such as guanine nucleotide exchange factors and GTPase-activating proteins shape these patterns by precisely controlling the spatio-temporal flux of Rho GTPase activity. Finally, we comment on additional mechanisms that might feed into the regulation of these signaling patterns and on novel technologies required to dissect this spatio-temporal complexity.

The most significant breakthrough in plant biotechnology is the development of the techniques to transform genes from unrelated sources into commercially important crop plants to develop resistance against targeted insect pests. The spatio-temporal expression of insecticidal genes in transgenic cotton varies with plant age, plant parts and environmental conditions. The understanding of this temporal and spatial variation in efficacy and the resulting mechanisms is essential for cotton protection and production. This review summarizes variations in the efficacy of introduced insecticidal genes in cotton crop. The factors contributing to the variability of endotoxins have also been highlighted. The reduction in Bt protein biosynthesis in late-season cotton tissues could be attributed to the overexpression of the Bt gene at earlier stages, which leads to gene regulation at post-transcription levels and consequently results in gene silencing at a later stage. Methylation of the promoter may also play a role in the declined expression of endotoxin proteins. In genetically modified crops several environmental factors have been reported to affect the expression of transgenes. Among environmental factors nitrogen metabolism, inhibition of synthesis, degradation, remobilization and high temperature are attributable to the quantitative reduction in Bt proteins. Applying plant growth regulators or protein enhancers such as Chaperone^TM may improve Bt cotton efficacy through enhancing the synthesis of proteins. Also some agronomic practices such as nitrogen fertilization and timely irrigation favour the endotoxin expression. Thus, variations in the efficacy of insecticidal genes in transgenic cotton and the involved mechanisms need to be understood fully so as to plan rational resistance management strategies to retard the rate of resistance development and to control target pests effectively by enhancing the endotoxin expression through genetic or agronomic management.

Multi-species conserved non-coding elements occur in the vertebrate genome and are clustered in the vicinity of developmentally regulated genes. Many are known to act as cis -regulators of transcription and may reside at long distances from the genes they regulate. However, the relationship of conserved sequence to encoded regulatory information and indeed, the mechanism by which these contribute to long-range transcriptional regulation is not well understood. The ZRS, a highly conserved cis -regulator, is a paradigm for such long-range gene regulation. The ZRS acts over approximately 1 Mb to control spatio-temporal expression of Shh in the limb bud and mutations within it result in a number of limb abnormalities, including polydactyly, tibial hypoplasia and syndactyly. We describe the activity of this developmental regulator and discuss a number of mechanisms by which regulatory mutations in this enhancer function to cause congenital abnormalities.

Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.

The Polo kinase is an essential regulator of cell division. Its ability to regulate multiple events at distinct subcellular locations and times during mitosis is remarkable. In the last few years, a much clearer mechanistic understanding of the functions and regulation of Polo in cell division has emerged. In this regard, the importance of coupling changes in activity with changes in localization is striking, both for Polo itself and for its upstream regulators. This review brings together several new pieces of the puzzle that are gradually revealing how Polo is regulated, in space and time, to enable its functions in the early stages of mitosis in animal cells. As a result, a unified view of how mitotic entry is spatio-temporally regulated is emerging.

Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response.

The ATR-Chk1 checkpoint pathway is activated by UV-induced DNA lesions and replication stress. Little was known about the spatio and temporal behaviour of the proteins involved, and we, therefore, examined the behaviour of the ATRIP-ATR and Rad9-Rad1-Hus1 putative DNA damage sensor complexes and the downstream effector kinase Chk1. We developed assays for the generation and validation of stable cell lines expressing GFP-fusion proteins. Photobleaching experiments in living cells expressing these fusions indicated that after UV-induced DNA damage, ATRIP associates more transiently with damaged chromatin than members of the Rad9-Rad1-Hus1 complex. Interestingly, ATRIP directly associated with locally induced UV damage, whereas Rad9 bound in a cooperative manner, which can be explained by the Rad17-dependent loading of Rad9 onto damaged chromatin. Although Chk1 dissociates from the chromatin upon UV damage, no change in the mobility of GFP-Chk1 was observed, supporting the notion that Chk1 is a highly dynamic protein.

Hox genes (HOX in humans), an evolutionary preserved gene family, are key determinants of embryonic development and cell memory gene program. Hox genes are organized in four clusters on four chromosomal loci aligned in 13 paralogous groups based on sequence homology (Hox gene network). During development Hox genes are transcribed, according to the rule of “spatio-temporal collinearity”, with early regulators of anterior body regions located at the 3’ end of each Hox cluster and the later regulators of posterior body regions placed at the distal 5’ end. The onset of 3’ Hox gene activation is determined by Wingless-type MMTV integration site family (Wnt) signaling, whereas 5’ Hox activation is due to paralogous group 13 genes, which act as posterior-inhibitors of more anterior Hox proteins (posterior prevalence). Deregulation of HOX genes is associated with developmental abnormalities and different human diseases. Paralogous HOX13 genes (HOX A13, HOX B13, HOX C13 and HOX D13) also play a relevant role in tumor development and progression. In this review, we will discuss the role of paralogous HOX13 genes regarding their regulatory mechanisms during carcinogenesis and tumor progression and their use as biomarkers for cancer diagnosis and treatment.

RNA-binding proteins (RBPs) are key regulators of transcription and translation, with highly dynamic spatio-temporal regulation. They are usually involved in the regulation of RNA splicing, polyadenylation, and mRNA stability and mediate processes such as mRNA localization and translation, thereby affecting the RNA life cycle and causing the production of abnormal protein phenotypes that lead to tumorigenesis and development. Accumulating evidence supports that RBPs play critical roles in vital life processes, such as bladder cancer initiation, progression, metastasis, and drug resistance. Uncovering the regulatory mechanisms of RBPs in bladder cancer is aimed at addressing the occurrence and progression of bladder cancer and finding new therapies for cancer treatment. This article reviews the effects and mechanisms of several RBPs on bladder cancer and summarizes the different types of RBPs involved in the progression of bladder cancer and the potential molecular mechanisms by which they are regulated, with a view to providing information for basic and clinical researchers.

Dans les organismes multicellulaires, plusieurs millier d’origines initient la réplication de l'ADN. Elles sont regroupées en domaines qui se répliquent tôt ou tard au cours de la phase S (origines précoces ou tardives). L'un des mécanismes régulant le programme de réplication est un point de contrôle intra phase S qui dépend des kinases ATR et Chk1. Cette voie est activée par un stress réplicatif engendré par le blocage des fourches de réplication aux origines précoces, en retour elle inhibe l’activation des origines tardives. Il a été proposé, que la protéine Polo-Like-Kinase 1 (Plk1) soit responsable du déclenchement des origines situées à proximité des fourches bloquées en cas de stress réplicatif. Cependant, aucune analyse de l’activation des origines n’a jamais été réalisée au cours d’une phase S non perturbée lorsque Plk1 est absente. Pour avoir une vue globale et unifiée du processus de réplication de l'ADN, des modèles numériques et analytiques ont été construits dans le passé, mais aucun d'eux n'intègrent le rôle de Chk1 et Plk1. L'objectif de ma thèse était d’étudier expérimentalement et analytiquement de quelle manière Chk1 peut réguler le déclenchement des origines dans l'espace et dans le temps. En particulier, de comprendre si Plk1 pouvait être impliquée dans cette régulation pendant une phase S non perturbée, à cette fin, j'ai utilisé le système réplicatif des extraits d’œuf de Xénopes. En premier lieu, j'ai intégré dans un modèle numérique l’action de Chk1 pour reproduire le programme de réplication du système Xénope. J'ai testé différents scénarios puis j’ai utilisé des données de peignage d'ADN obtenues précédemment dans des conditions d'inhibition de la kinase Chk1. Les simulations Monte Carlo obtenues ont été ajustées aux données expérimentales en optimisant les valeurs des paramètres libres des modèles. J'ai trouvé qu'il fallait ajouter deux hypothèses aux modèles de réplication développés précédemment: 1) la présence d’une forte inhibition du déclenchement des origines par Chk1 à partir du début de la phase S 2) la présence de domaines génomiques répliquant précocement et qui échappent à cette inhibition. Deuxièmement, j'ai montré expérimentalement que, Plk1 actif est recrutée sur la chromatine avant le début de la phase S non perturbée et qu'en l'absence de Plk1, la réplication de l'ADN est ralentie. De plus, l’absence de Plk1 entraîne une augmentation de la phosphorylation de Chk1 et une diminution de l’activité de la kinase Cdk2, ce qui suggère que Plk1 inhibe Chk1. En réalisant des expériences de peignage d’ADN, j'ai démontré qu’en l’absence de Plk1 on observe une baisse du niveau d’activation des origines. L'analyse de ces données par mon modèle numérique suggère que Plk1 régule négativement l’action de Chk1 levant ainsi son action inhibitrice sur l’activation globale des origines. Cet effet concorde avec mes observations expérimentales. Il semble cependant que Plk1 n’agisse pas à proximité directe des fourches de réplication, comme cela avait été proposé précédemment. Enfin, en assimilant le processus de réplication à un processus de nucléation et de croissance unidimensionnel, j'ai développé une nouvelle approche quantitative pour étudier la régulation du programme de réplication. Cette approche lie la similarité entre les profils spatiaux de réplication d'une molécule unique et les processus de régulation de la réplication de l'ADN. En analysant les données de peignage d'ADN, j'ai montré que le programme de réplication de l'ADN des embryons précoces de Xénope est régulé par deux processus exclusifs dans l'espace et dans le temps. L’un avec une fréquence faible d’activation des origines et une vitesse apparente de fourches élevée et un second, régulé par Plk1, présentant une fréquence d’activation élevée des origines avec une vitesse apparente de fourches faible
The initiation of DNA replication in multicellular organisms starts from several thousand genomic loci called replication origins. They are grouped into domains which replicate early or late during S phase. The firing of a replication origin creates two diverging replication forks that replicate flanking DNA. One of the mechanisms regulating DNA replication program is the ATR/Chk1 dependent intra-S phase checkpoint. This pathway is activated by replicative stress due to stalled replication forks at early firing origins and in turn, inhibits the late firing of origins. It has been proposed that the checkpoint recovery kinase Plk1 (Polo-Like-Kinase 1) could be responsible for allowing origin firing close to stalled forks in replication stress conditions. However, origin firing has not been analysed after Plk1 inhibition or depletion during unperturbed S phase. To assemble a comprehensive and unified view of the DNA replication process numerical and analytical models have been built in the past, but none of them integrates the role of checkpoint pathways. The goal of my thesis was to investigate experimentally and analytically how the checkpoint regulates the firing of origins in space and time and, in particular, whether the Plk1 is implicated in the regulation of origin firing during unperturbed S phase. To this end, I used the Xenopus in vitro system. First, I integrated in a numerical model the checkpoint pathway to describe the replication program in the Xenopus in vitro system. I tested different scenarios and used DNA combing data previously obtained by the laboratory after the inhibition of the checkpoint kinase Chk1. Monte Carlo simulated data were fitted to experimental data by optimizing the values of free parameters of models using a genetic algorithm. I found that two new hypothesis should be added to formerly built replication models: 1) a strong inhibition of origin firing by Chk1 from the beginning of S phase 2) the presence of early replicating genomic domains that evade the origin firing inhibition. Second, I experimentally showed that during unperturbed S phase active Plk1 is recruited to chromatin before the start of S phase and that in the absence of Plk1, DNA replication is slowed down. Moreover, Plk1 depletion led to an increase in Chk1 phosphorylation (p-Chk1) and a decrease of Cdk2 activity, suggesting that Plk1 inhibits the intra-S phase checkpoint. Performing DNA combing, I demonstrated that Plk1 depletion leads to a decrease in origin firing level. Analysis of the combing data by the developed numerical model suggested that during unchallenged S phase Plk1 down regulates the global origin firing inhibitory action of Chk1, consistent with the experimental observation of increased level of p-Chk1 in Plk1 depleted Xenopus egg extract. However, Plk1 does not seem to act close to replication forks as was proposed earlier. Finally, by considering replication process as a one-dimensional nucleation and growth process and using statistical methods, I developed a new quantitative approach to study the regulation of replication program. This approach links the similarity between single molecule replication patterns to DNA replication regulating processes. By analyzing DNA combing data, I showed that DNA replication program in Xenopus early embryos is regulated by two spatially and temporally exclusive processes. One with low frequency of origin firing and high apparent fork speed and a second, controlled by PlK1, with a high frequency of origin firing and a low apparent fork speed. Altogether my results demonstrate that Plk1 positively regulates replication origin firing during normal S phase by down regulating the replication checkpoint. The numerical model predicts the existence of replication timing domains in the Xenopus model system. Future work will show whether Plk1 regulates the replication program at the level of genomic domains

This thesis draws on David Harvey’s concept of “accumulation by dispossession” and an international political economy (IPE) approach centred on the institutional arrangements and power structures that privilege certain actors and values, in order to critique current capitalist practices of primitive accumulation by the global corporate extractive industry. The thesis examines how accumulation by dispossession by the global extractive industry is facilitated by the “free entry” or “free mining” principle. It does so by focusing on Canada as a leader in the global extractive industry and the spread of this country’s mining laws to other countries – in other words, the transnationalisation of norms in the global extractive industry – so as to maintain a consistent and familiar operating environment for Canadian extractive companies. The transnationalisation of norms is further promoted by key international institutions such as the World Bank, which is also the world’s largest development lender and also plays a key role in shaping the regulations that govern natural resource extraction. The thesis briefly investigates some Canadian examples of resource extraction projects, in order to demonstrate the weaknesses of Canadian mining laws, particularly the lack of protection of landowners’ rights under the free entry system and the subsequent need for “free, prior and informed consent” (FPIC). The thesis also considers some of the challenges to the adoption and implementation of the right to FPIC. These challenges include embedded institutional structures like the free entry mining system, international political economy (IPE) as shaped by international institutions and powerful corporations, as well as concerns regarding ‘local’ power structures or the legitimacy of representatives of communities affected by extractive projects. The thesis concludes that in order for Canada to be truly recognized as a leader in the global extractive industry, it must establish legal norms domestically to ensure that Canadian mining companies and residents can be held accountable when there is evidence of environmental and/or human rights violations associated with the activities of Canadian mining companies abroad. The thesis also concludes that Canada needs to address underlying structural issues such as the free entry mining system and implement FPIC, in order to curb “accumulation by dispossession” by the extractive industry, both domestically and abroad.

This paper focuses on simulating environmental impacts on grapevine behavioral dynamics and vineyard management strategies. The methodology presented uses technology from geomatics object oriented databases and spatio-temporal data models. Our approach has two principle objectives, first, to simulate grapevine phenology and grape ripening under spatial and temporal environmental conditions and constraints and secondly, to simulate viticultural practices and adaptation strategies under various constraints (environmental, economical, socio-technical). The approach is based on a responsive agent-based structure where environmental conditions and constraints are considered as a set of forcing data (biophysical, socio-economic and regulatory data) that influences the modelled activities. The experiment was conducted in the regulated wine producing appellation Grand Cru “Quarts de Chaume”, situated in the middle Loire Valley, France. All of the methodology, from the implementation of the knowledge database to the analysis of the first simulation, is presented in this paper.

The dynamics of land use/land cover (LU/LC) is a manifestation of the cyclic correlation among the kind and magnitude of causes, impacts, responses and resulting ecological processes of the ecosystem. Thus, the holistic understanding of the complex mechanisms that control LU/LC requires synergetic adoption of measurement approaches, addressing issues, and identifying drivers of change and state of art technologies for mitigation measures. As the spatio-temporal heterogeneity of the LU/LC increases, its impact on biodiversity becomes even more difficult to anticipate. Thus, in order to understand the spatio-temporal dynamics of change in landscape and its relationship to biodiversity, it is necessary to reliably identify and quantify the indicators of change. In addition, it is also important to have better understanding of the technologies and techniques that serve as complimentary tool for land mitigation and conservation planning. Against this background, the chapter aims to synthesize LU/LC studies worldwide and their impacts on biodiversity. This chapter explores identification and analysis of key natural, socio-economic and regulatory drivers for LU/LC. Finally, it attempts to collate some LU/LC studies involving usage of geospatial tools, such as satellite remote sensing, Geographic Information System (GIS), Global Positioning System (GPS), and integrative tools, besides conventional approaches that could assist decision makers, land managers, stakeholders and researchers in better management and formulation of conservation strategies based on scientific grounds.

When demand increases beyond the system capacity, riders in ride-hailing/ride-sharing systems often experience long waiting time, resulting in poor customer satisfaction. This paper proposes a spatio-temporal pricing framework (AP-RTRS) to alleviate this challenge and shows how it naturally complements state-of-the-art dispatching and routing algorithms. Specifically, the pricing optimization model regulates demand to ensure that every rider opting to use the system is served within reason-able time: it does so either by reducing demand to meet the capacity constraints or by prompting potential riders to postpone service to a later time. The pricing model is a model-predictive control algorithm that works at a coarser temporal and spatial granularity compared to the real-time dispatching and routing, and naturally integrates vehicle relocations. Simulation experiments indicate that the pricing optimization model achieves short waiting times without sacrificing revenues and geographical fairness.