Temporal Program Research Articles

Virtual-Reality Training of Elite Boxers Preparing for the Tokyo 2020 Olympics During the COVID-19 Pandemic: A Case Study

The COVID-19 pandemic struck right during the Olympic preparation, leading to significant training restrictions such as noncontact practices for combat sports. This case study research describes the application of a complementary virtual-reality (VR) intervention to train elite boxers preparing for Tokyo 2020 during the pandemic. It also addresses the evaluation of broader visuocognitive functions in elite boxers. Six boxers were allocated to two groups: one experimental group trained on a 360° VR (360VR) temporal video-occlusion program, and one active control group trained on a VR game simulation during 11 sessions. Pre- and postevaluations of specific decision-making performance were performed on a 360VR evaluation test. Fundamental visual and visuocognitive functions were assessed at baseline. Greater on-test decision-making improvements were observed in the 360VR-trained group compared with VR game, and 360VR offered self-reported satisfactory, representative, and safe individual training opportunities for the boxers. More research is warranted to explore the applications of 360VR and VR simulation for psycho-perceptual-motor-skill evaluation and training. Superior visuocognitive performance was observed in elite boxers and should also be a topic of further investigation. The methodological approach, implementation, and reflections are provided in detail to guide practitioners toward the applied use of VR in the sporting environment.

The Nature of the Fungal Cargo Induces Significantly Different Temporal Programmes of Macrophage Phagocytosis

The Nature of the Fungal Cargo Induces Significantly Different Temporal Programmes of Macrophage Phagocytosis

Linear-Time Temporal Answer Set Programming

AbstractIn this survey, we present an overview on (Modal) Temporal Logic Programming in view of its application to Knowledge Representation and Declarative Problem Solving. The syntax of this extension of logic programs is the result of combining usual rules with temporal modal operators, as in Linear-time Temporal Logic (LTL). In the paper, we focus on the main recent results of the non-monotonic formalism called Temporal Equilibrium Logic (TEL) that is defined for the full syntax of LTL but involves a model selection criterion based on Equilibrium Logic, a well known logical characterization of Answer Set Programming (ASP). As a result, we obtain a proper extension of the stable models semantics for the general case of temporal formulas in the syntax of LTL. We recall the basic definitions for TEL and its monotonic basis, the temporal logic of Here-and-There (THT), and study the differences between finite and infinite trace length. We also provide further useful results, such as the translation into other formalisms like Quantified Equilibrium Logic and Second-order LTL, and some techniques for computing temporal stable models based on automata constructions. In the remainder of the paper, we focus on practical aspects, defining a syntactic fragment called (modal) temporal logic programs closer to ASP, and explaining how this has been exploited in the construction of the solver telingo, a temporal extension of the well-known ASP solver clingo that uses its incremental solving capabilities.

Quantum Information in Relativity: The Challenge of QFT Measurements.

Proposed quantum experiments in deep space will be able to explore quantum information issues in regimes where relativistic effects are important. In this essay, we argue that a proper extension of quantum information theory into the relativistic domain requires the expression of all informational notions in terms of quantum field theoretic (QFT) concepts. This task requires a working and practicable theory of QFT measurements. We present the foundational problems in constructing such a theory, especially in relation to longstanding causality and locality issues in the foundations of QFT. Finally, we present the ongoing Quantum Temporal Probabilities program for constructing a measurement theory that (i) works, in principle, for any QFT, (ii) allows for a first- principles investigation of all relevant issues of causality and locality, and (iii) it can be directly applied to experiments of current interest.

A shared transcriptional code orchestrates temporal patterning of the central nervous system.

The molecular mechanisms that produce the full array of neuronal subtypes in the vertebrate nervous system are incompletely understood. Here, we provide evidence of a global temporal patterning program comprising sets of transcription factors that stratifies neurons based on the developmental time at which they are generated. This transcriptional code acts throughout the central nervous system, in parallel to spatial patterning, thereby increasing the diversity of neurons generated along the neuraxis. We further demonstrate that this temporal program operates in stem cell-derived neurons and is under the control of the TGFβ signaling pathway. Targeted perturbation of components of the temporal program, Nfia and Nfib, reveals their functional requirement for the generation of late-born neuronal subtypes. Together, our results provide evidence for the existence of a previously unappreciated global temporal transcriptional program of neuronal subtype identity and suggest that the integration of spatial and temporal patterning mechanisms diversifies and organizes neuronal subtypes in the vertebrate nervous system.

Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 tsc229 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program. We find that P22 tsc229 excises early after induction, but P22 delays excision to just before it is detrimental to phage production. This allows P22 to engage in lateral transduction. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.

A Protocol for Genome-Wide Analysis of DNA Replication Timing in Intact Root Tips.

DNA replication during Sphase in eukaryotes is a highly regulated process that ensures the accurate transmission of genetic material to daughter cells during cell division. Replication follows a well-defined temporal program, which has been studied extensively in humans, Drosophila, and yeast, where it is clear that the replication process is both temporally and spatially ordered. The replication timing (RT) program is increasingly considered to be a functional readout of genomic features and chromatin organization. Although there is increasing evidence that plants display important differences in their DNA replication process compared to animals, RT programs in plants have not been extensively studied. To address this deficiency, we developed an improved protocol for the genome-wide RT analysis by sequencing newly replicated DNA ("Repli-seq") and applied it to the characterization of RT in maize root tips. Our protocol uses 5-ethynyl-2'-deoxyuridine (EdU) to label replicating DNA in vivo in intact roots. Our protocol also eliminates the need for synchronization and frequently associated chemical perturbations as well as the need for cell cultures, which can accumulate genetic and epigenetic differences over time. EdU can be fluorescently labeled under mild conditions and does not degrade subnuclear structure, allowing for the differentiation of labeled and unlabeled nuclei by flow sorting, effectively eliminating contamination issues that can result from sorting on DNA content alone. We also developed an analysis pipeline for analyzing and classifying regions of replication and present it in a point-and-click application called Repliscan that eliminates the need for command line programming.

Genetic dissection of the glutamatergic neuron system in cerebral cortex

Diverse types of glutamatergic pyramidal neurons mediate the myriad processing streams and output channels of the cerebral cortex1,2, yet all derive from neural progenitors of the embryonic dorsal telencephalon3,4. Here we establish genetic strategies and tools for dissecting and fate-mapping subpopulations of pyramidal neurons on the basis of their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable the combinatorial targeting of major progenitor types and projection classes. Combinatorial strategies confer viral access to subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons that assemble cortical processing networks and output channels.

Radiation-Induced Macrophage Senescence Impairs Resolution Programs and Drives Cardiovascular Inflammation.

Radiation is associated with tissue damage and increased risk of atherosclerosis, but there are currently no treatments and a very limited mechanistic understanding of how radiation impacts tissue repair mechanisms. We uncovered that radiation significantly delayed temporal resolution programs that were associated with decreased efferocytosis in vivo. Resolvin D1 (RvD1), a known proresolving ligand, promoted swift resolution and restored efferocytosis in sublethally irradiated mice. Irradiated macrophages exhibited several features of senescence, including increased expression of p16INK4A and p21, heightened levels of SA-β-gal, COX-2, several proinflammatory cytokines/chemokines, and oxidative stress (OS) in vitro, and when transferred to mice, they exacerbated inflammation in vivo. Mechanistically, heightened OS in senescent macrophages led to impairment in their ability to carry out efficient efferocytosis, and treatment with RvD1 reduced OS and improved efferocytosis. Sublethally irradiated Ldlr -/- mice exhibited increased plaque necrosis, p16INK4A cells, and decreased lesional collagen compared with nonirradiated controls, and treatment with RvD1 significantly reduced necrosis and increased lesional collagen. Removal of p16INK4A hematopoietic cells during advanced atherosclerosis with p16-3MR mice reduced plaque necrosis and increased production of key intraplaque-resolving mediators. Our results demonstrate that sublethal radiation drives macrophage senescence and efferocytosis defects and suggest that RvD1 may be a new therapeutic strategy to limit radiation-induced tissue damage.

The branching orders of the crown of virginal tree of Ulmus glabra Huds

Tree crown formation in ontogenesis is a realization of spatial and temporal development program. Based on the study of young individuals of U. glabra growing in a natural oak forest, the presence of two groups of axes was shown. One group creates the axes of crown base - “skeleton”. The other one appears at a certain age and creates the so-called “crown lace” - a short-lived and replaceable base for photosynthesis. The transition from the formation of the skeletal part of the crown to the next stage, which occurs in the 4th branching order, the shoots of which are significantly shorter, and their number is greater, is quantitatively shown. It is shown that the lengths and number of leaves on shoots in the axes of the first three orders of branching vary within a large range. The maximum variability is reached on the third order of branching, after which it decreases. When crown development reaches the 4th order, spatial growth limitations, which are determined by angles of shoot branching, leaf size, lifetime of axes and shoots, begin to play their roles. Here, more structured crown space is required to optimize the photosynthetic surface.

Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics.

How do cells perceive time? Do cells use temporal information to regulate the production/degradation of their enzymes, membranes, and organelles? Does controlling biological time influence cytoskeletal organization and cellular architecture in ways that confer evolutionary and physiological advantages? Potential answers to these fundamental questions of cell biology have historically revolved around the discussion of ‘master’ temporal programs, such as the principal cyclin-dependent kinase/cyclin cell division oscillator and the circadian clock. In this review, we provide an overview of the recent evidence supporting an emerging concept of ‘autonomous clocks,’ which under normal conditions can be entrained by the cell cycle and/or the circadian clock to run at their pace, but can also run independently to serve their functions if/when these major temporal programs are halted/abrupted. We begin the discussion by introducing recent developments in the study of such clocks and their roles at different scales and complexities. We then use current advances to elucidate the logic and molecular architecture of temporal networks that comprise autonomous clocks, providing important clues as to how these clocks may have evolved to run independently and, sometimes at the cost of redundancy, have strongly coupled to run under the full command of the cell cycle and/or the circadian clock. Next, we review a list of important recent findings that have shed new light onto potential hallmarks of autonomous clocks, suggestive of prospective theoretical and experimental approaches to further accelerate their discovery. Finally, we discuss their roles in health and disease, as well as possible therapeutic opportunities that targeting the autonomous clocks may offer.

DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability

The DNA polymerase zeta (Polζ) plays a critical role in bypassing DNA damage. REV3L, the catalytic subunit of Polζ, is also essential in mouse embryonic development and cell proliferation for reasons that remain incompletely understood. In this study, we reveal that REV3L protein interacts with heterochromatin components including repressive histone marks and localizes in pericentromeric regions through direct interaction with HP1 dimer. We demonstrate that Polζ/REV3L ensures progression of replication forks through difficult‐to‐replicate pericentromeric heterochromatin, thereby preventing spontaneous chromosome break formation. We also find that Rev3l‐deficient cells are compromised in the repair of heterochromatin‐associated double‐stranded breaks, eliciting deletions in late‐replicating regions. Lack of REV3L leads to further consequences that may be ascribed to heterochromatin replication and repair‐associated functions of Polζ, with a disruption of the temporal replication program at specific loci. This is correlated with changes in epigenetic landscape and transcriptional control of developmentally regulated genes. These results reveal a new function of Polζ in preventing chromosome instability during replication of heterochromatic regions.

Controlling Polymer Molecular Weight Distribution through a Latent Mediator Strategy with Temporal Programming

AbstractPolymer molecular weight distribution (MWD) is a key parameter of polymers. Here we present a robust method for controlling polymer MWD in controlled cationic polymerizations. A latent mediator strategy was designed and combined with temporal programming to regenerate mediators at different times during polymerization. Both the breadths and shapes of MWD curves were tuned easily by adjusting an external light source. Bimodal, trimodal, and tetramodal distributions were obtained, and the breadths could be varied from 1.06 to 2.09. Polymers with different MWDs prepared by this method had good chain end fidelity, which was demonstrated with successful chain‐extension experiments. In addition, the introduction of temporal programming with a computer‐controlled single chip for the light source opened an avenue for the use of artificial intelligence in polymer synthesis.

Controlling Polymer Molecular Weight Distribution through a Latent Mediator Strategy with Temporal Programming.

Polymer molecular weight distribution (MWD) is a key parameter of polymers. Here we present a robust method for controlling polymer MWD in controlled cationic polymerizations. A latent mediator strategy was designed and combined with temporal programming to regenerate mediators at different times during polymerization. Both the breadths and shapes of MWD curves were tuned easily by adjusting an external light source. Bimodal, trimodal, and tetramodal distributions were obtained, and the breadths could be varied from 1.06 to 2.09. Polymers with different MWDs prepared by this method had good chain end fidelity, which was demonstrated with successful chain-extension experiments. In addition, the introduction of temporal programming with a computer-controlled single chip for the light source opened an avenue for the use of artificial intelligence in polymer synthesis.

An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles.

Recent results comparing the temporal program of genome replication of yeast species belonging to the Lachancea clade support the scenario that the evolution of the replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins and use it to identify the evolutionary biases that shape the replication timing profiles. Comparing different evolutionary models with data, we find that replication origin birth and death events are mainly driven by two evolutionary pressures, the first imposes that events leading to higher double-stall probability of replication forks are penalized, while the second makes less efficient origins more prone to evolutionary loss. This analysis provides an empirically grounded predictive framework for quantitative evolutionary studies of the replication timing program.

RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators

Plasma cells (PCs) play an important role in the adaptive immune system through a continuous production of antibodies. We have demonstrated that PC differentiation can be modeled in vitro using complex multistep culture systems reproducing sequential differentiation process occurring in vivo. Here we present a comprehensive, temporal program of gene expression data encompassing human PC differentiation (PCD) using RNA sequencing (RNA-seq). Our results reveal 6374 differentially expressed genes classified into four temporal gene expression patterns. A stringent pathway enrichment analysis of these gene clusters highlights known pathways but also pathways largely unknown in PCD, including the heme biosynthesis and the glutathione conjugation pathways. Additionally, our analysis revealed numerous novel transcriptional networks with significant stage-specific overexpression and potential importance in PCD, including BATF2, BHLHA15/MIST1, EZH2, WHSC1/MMSET, and BLM. We have experimentally validated a potent role for BLM in regulating cell survival and proliferation during human PCD. Taken together, this RNA-seq analysis of PCD temporal stages helped identify coexpressed gene modules with associated up/downregulated transcription regulator genes that could represent major regulatory nodes for human PC maturation. These data constitute a unique resource of human PCD gene expression programs in support of future studies for understanding the underlying mechanisms that control PCD.

Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons.

Neurogenesis in the developing neocortex begins with the generation of the preplate, which consists of early-born neurons including Cajal-Retzius (CR) cells and subplate neurons. Here, utilizing the Ebf2-EGFP transgenic mouse in which EGFP initially labels the preplate neurons then persists in CR cells, we reveal the dynamic transcriptome profiles of early neurogenesis and CR cell differentiation. Genome-wide RNA-seq and ChIP-seq analyses at multiple early neurogenic stages have revealed the temporal gene expression dynamics of early neurogenesis and distinct histone modification patterns in early differentiating neurons. We have identified a new set of coding genes and lncRNAs involved in early neuronal differentiation and validated with functional assays in vitro and in vivo. In addition, at E15.5 when Ebf2-EGFP+ cells are mostly CR neurons, single-cell sequencing analysis of purified Ebf2-EGFP+ cells uncovers molecular heterogeneities in CR neurons, but without apparent clustering of cells with distinct regional origins. Along a pseudotemporal trajectory these cells are classified into three different developing states, revealing genetic cascades from early generic neuronal differentiation to late fate specification during the establishment of CR neuron identity and function. Our findings shed light on the molecular mechanisms governing the early differentiation steps during cortical development, especially CR neuron differentiation.

PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.

ABSTRACTRadial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here, we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phase of neurogenesis in the mouse neocortex. Loss of Prdm16 delays the timely progression of RG, leading to defective cortical laminar organization. Our genomic analyses demonstrate that PRDM16 regulates a subset of genes that are dynamically expressed between early and late neurogenesis. We show that PRDM16 suppresses target gene expression through limiting chromatin accessibility of permissive enhancers. We further confirm that crucial target genes regulated by PRDM16 are neuronal specification genes, cell cycle regulators and molecules required for neuronal migration. These findings provide evidence to support the finding that neural progenitors temporally shift the gene expression program to achieve neural cell diversity.

Autonomous Shapeshifting Hydrogels via Temporal Programming of Photoswitchable Dynamic Network

Responsive materials typically require external stimulation for triggering. In contrast, temporal programmable materials exhibit autonomous trigger-free responses that are uniquely attractive. Its largely under-explored molecular enabling mechanisms, however, prohibit its expansion into functionally diverse devices. We illustrate here that the dynamic ionic bonds within a tough hydrogel can be an effective and generally applicable mechanism for temporal programming. This leads to an unusual shapeshifting behavior that can be precisely manipulated without requiring any external triggering. Further incorporation of photoswitchable dynamic disulfide bonds in the hydrogel network introduces another mechanism for the spatial control of the geometric shapeshifting pathway. The synergistic effect of temporal programmability and photodefinability allows access to multifunctional shapeshifting devices with versatility beyond conventional systems.

A novel role for Dun1 in the regulation of origin firing upon hyper-acetylation of H3K56.

During DNA replication newly synthesized histones are incorporated into the chromatin of the replicating sister chromatids. In the yeast Saccharomyces cerevisiae new histone H3 molecules are acetylated at lysine 56. This modification is carefully regulated during the cell cycle, and any disruption of this process is a source of genomic instability. Here we show that the protein kinase Dun1 is necessary in order to maintain viability in the absence of the histone deacetylases Hst3 and Hst4, which remove the acetyl moiety from histone H3. This lethality is not due to the well-characterized role of Dun1 in upregulating dNTPs, but rather because Dun1 is needed in order to counteract the checkpoint kinase Rad53 (human CHK2) that represses the activity of late firing origins. Deletion of CTF18, encoding the large subunit of an alternative RFC-like complex (RLC), but not of components of the Elg1 or Rad24 RLCs, is enough to overcome the dependency of cells with hyper-acetylated histones on Dun1. We show that the detrimental function of Ctf18 depends on its interaction with the leading strand polymerase, Polε. Our results thus show that the main problem of cells with hyper-acetylated histones is the regulation of their temporal and replication programs, and uncover novel functions for the Dun1 protein kinase and the Ctf18 clamp loader.