scholarly journals Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
José Muñoz-Dorado ◽  
Aurelio Moraleda-Muñoz ◽  
Francisco Javier Marcos-Torres ◽  
Francisco Javier Contreras-Moreno ◽  
Ana Belen Martin-Cuadrado ◽  
...  
Keyword(s):  
Myxococcus Xanthus ◽  
Developmental Cycle ◽  
Fruiting Bodies ◽  
Rna Seq ◽  
Specific Time ◽  
Future Studies ◽  
Developmental Program ◽  
Global View ◽  
Specific Time Point ◽  
Time Point

The bacterium Myxococcus xanthus exhibits a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the transcriptome of the 96 hr developmental program. These data revealed that 1415 genes were sequentially expressed in 10 discrete modules, with expression peaking during aggregation, in the transition from aggregation to sporulation, or during sporulation. Analysis of genes expressed at each specific time point provided insights as to how starving cells obtain energy and precursors necessary for assembly of fruiting bodies and into developmental production of secondary metabolites. This study offers the first global view of developmental transcriptional profiles and provides important tools and resources for future studies.

scholarly journals Global transcriptome analysis of theMyxococcus xanthusmulticellular developmental program

2019 ◽  
Author(s):  
J. Muñoz-Dorado ◽  
A. Moraleda-Muñoz ◽  
F.J. Marcos-Torres ◽  
F.J. Contreras-Moreno ◽  
A.B. Martin-Cuadrado ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Myxococcus Xanthus ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Developmental Cycle ◽  
Fruiting Bodies ◽  
Rna Seq ◽  
Developmental Program ◽  
Specific Time Point ◽  
Global Transcriptome

ABSTRACTThe bacteriaMyxococcus xanthusexhibit a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the global transcriptome of the 96 h developmental program. This data revealed that many genes were sequentially expressed in discrete modules, with expression peaking during aggregation, in the transition from aggregation to sporulation, or during sporulation. Analysis of genes expressed at each specific time point provided a global framework integrating regulatory factors coordinating motility and differentiation in the developmental program. These data provided insights as to how starving cells obtain energy and precursors necessary for assembly of fruiting bodies and into developmental production of secondary metabolites. This study offers the first global view of developmental transcriptional profiles and provides an important scaffold for future studies.IMPACT STATEMENTInvestigation of global gene expression profiles during formation of theMyxococcus xanthusspecialized biofilm reveals a genetic regulatory network that coordinates cell motility, differentiation, and secondary metabolite production.

scholarly journals Consistency in mutualism relies on local, rather than wider community biodiversity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Katie Dunkley ◽  
Jo Cable ◽  
Sarah E. Perkins
Keyword(s):  
Biodiversity Loss ◽  
Context Dependency ◽  
Third Party ◽  
Interaction Patterns ◽  
Specific Time ◽  
Specific Time Point ◽  
Service Resource ◽  
Resource Mutualism ◽  
Time Point

AbstractMutualistic interactions play a major role in shaping the Earth’s biodiversity, yet the consistent drivers governing these beneficial interactions are unknown. Using a long-term (8 year, including > 256 h behavioural observations) dataset of the interaction patterns of a service-resource mutualism (the cleaner-client interaction), we identified consistent and dynamic predictors of mutualistic outcomes. We showed that cleaning was consistently more frequent when the presence of third-party species and client partner abundance locally increased (creating choice options), whilst partner identity regulated client behaviours. Eight of our 12 predictors of cleaner and client behaviour played a dynamic role in predicting both the quality (duration) and quantity (frequency) of interactions, and we suggest that the environmental context acting on these predictors at a specific time point will indirectly regulate their role in cleaner-client interaction patterns: context-dependency can hence regulate mutualisms both directly and indirectly. Together our study highlights that consistency in cleaner-client mutualisms relies strongly on the local, rather than wider community—with biodiversity loss threatening all environments this presents a worrying future for the pervasiveness of mutualisms.

scholarly journals Estimating the Necessary Amount of Driving Data for Assessing Driving Behavior

Sensors ◽  
2020 ◽  
Vol 20 (9) ◽  
pp. 2600 ◽  
Author(s):  
Anna-Maria Stavrakaki ◽  
Dimitrios I. Tselentis ◽  
Emmanouil Barmpounakis ◽  
Eleni I. Vlahogianni ◽  
George Yannis
Keyword(s):  
Discrete Time ◽  
Driving Behavior ◽  
Methodological Framework ◽  
Detailed Data ◽  
Specific Time ◽  
Speed Limits ◽  
Specific Time Point ◽  
Smartphone Sensors ◽  
Over Time ◽  
Time Point

The aim of this paper was to provide a methodological framework for estimating the amount of driving data that should be collected for each driver in order to acquire a clear picture regarding their driving behavior. We examined whether there is a specific discrete time point for each driver, in the form of total driving duration and/or the number of trips, beyond which the characteristics of driving behavior are stabilized over time. Various mathematical and statistical methods were employed to process the data collected and determine the time point at which behavior converges. Detailed data collected from smartphone sensors are used to test the proposed methodology. The driving metrics used in the analysis are the number of harsh acceleration and braking events, the duration of mobile usage while driving and the percentage of time driving over the speed limits. Convergence was tested in terms of both the magnitude and volatility of each metric for different trips and analysis is performed for several trip durations. Results indicated that there is no specific time point or number of trips after which driving behavior stabilizes for all drivers and/or all metrics examined. The driving behavior stabilization is mostly affected by the duration of the trips examined and the aggressiveness of the driver.

scholarly journals σ54 Enhancer Binding Proteins and Myxococcus xanthus Fruiting Body Development

2004 ◽  
Vol 186 (13) ◽  
pp. 4361-4368 ◽  
Author(s):  
Jimmy S. Jakobsen ◽  
Lars Jelsbak ◽  
Lotte Jelsbak ◽  
Roy D. Welch ◽  
Craig Cummings ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Binding Proteins ◽  
Myxococcus Xanthus ◽  
Fruiting Bodies ◽  
Knockout Mutant ◽  
Developmentally Regulated ◽  
Enhancer Binding Proteins ◽  
Developmental Program ◽  
Body Development ◽  
Fruiting Body Development

ABSTRACT A search of the M1genome sequence, which includes 97% of the Myxococcus xanthus genes, identified 53 sequence homologs of σ54-dependent enhancer binding proteins (EBPs). A DNA microarray was constructed from the M1genome that includes those homologs and 318 other M. xanthus genes for comparison. To screen the developmental program with this array, an RNA extract from growing cells was compared with one prepared from developing cells at 12 h. Previous reporter studies had shown that M. xanthus has initiated development and has begun to express many developmentally regulated genes by 12 h. The comparison revealed substantial increases in the expression levels of 11 transcription factors that may respond to environmental stimuli. Six of the 53 EBP homologs were expressed at significantly higher levels at 12 h of development than during growth. Three were previously unknown genes, and they were inactivated to look for effects on fruiting body development. One knockout mutant produced fruiting bodies of abnormal shape that depended on the composition of the medium.

scholarly journals Imputation algorithm using copulas

2006 ◽  
Vol 3 (1) ◽  
Author(s):  
Ene Käärik
Keyword(s):  
Conditional Distribution ◽  
Joint Distribution ◽  
Missing Values ◽  
Repeated Measurements ◽  
Specific Time ◽  
Marginal Distributions ◽  
Specific Time Point ◽  
Compound Symmetry ◽  
Time Point

In this paper the author demonstrates how the copulas approach can be used to find algorithms for imputing dropouts in repeated measurements studies. One problem with repeated measurements is the knowledge that the data is described by joint distribution. Copulas are used to create the joint distribution with given marginal distributions. Knowing the joint distribution we can find the conditional distribution of the measurement at a specific time point, conditioned by past measurements, and this will be essential for imputing missing values. Using Gaussian copulas, two simple methods for imputation are presented. Compound symmetry and the case of autoregressive dependencies are discussed. Effectiveness of the proposed approach is tested via series of simulations and results showing that the imputation algorithms based on copulas are appropriate for modelling dropouts.

Developmental toxicity of flucytosine following administration to pregnant rats at a specific time point of organogenesis

2018 ◽  
Vol 59 (2) ◽  
pp. 39-42 ◽  
Author(s):  
Sakiko Fujii ◽  
Kaoru Yabe ◽  
Yuki Kariwano-Kimura ◽  
Masatoshi Furukawa ◽  
Kouta Itoh ◽  
...  
Keyword(s):  
Developmental Toxicity ◽  
Specific Time ◽  
Pregnant Rats ◽  
Specific Time Point ◽  
Time Point

I-states-as-objects-analysis (ISOA): Extensions of an approach to studying short-term developmental processes by analyzing typical patterns

2012 ◽  
Vol 36 (3) ◽  
pp. 237-246 ◽  
Author(s):  
Lars R. Bergman ◽  
Jari-Erik Nurmi ◽  
Alexander A. von Eye
Keyword(s):  
Longitudinal Data ◽  
Developmental Stability ◽  
Specific Time ◽  
Short Term ◽  
Classification Analysis ◽  
Stability And Change ◽  
Children's Achievement ◽  
Specific Time Point ◽  
Time Invariant ◽  
Time Point

I-states-as-objects-analysis (ISOA) is a person-oriented methodology for studying short-term developmental stability and change in patterns of variable values. ISOA is based on longitudinal data with the same set of variables measured at all measurement occasions. A key concept is the i-state, defined as a person’s pattern of variable values at a specific time point. All i-states are first subjected to a classification analysis that results in a time-invariant classification characterized by a number of typical i-states. Each person is then characterized at each time point by the typical i-state he/she belongs to. Then the person’s sequences of typical i-states are analyzed with regard to structural and individual stability and change. Extensions of ISOA are presented where: (1) some methods for checking the assumption of a time-invariant classification are indicated; (2) information about the degree of dissimilarity between typical i-states is used as an aid in interpreting the findings; and (3) attention is given to closed paths—that is, typical i-state sequences that do not occur at all. To demonstrate the methods, an empirical example is given that concerns the development of children’s achievement-intelligence patterns between ages 10 and 13.

The ecology of social time: An outline of an empirical analytic framework of the sociology of time

2015 ◽  
Vol 26 (2) ◽  
pp. 137-164 ◽  
Author(s):  
Tsuo-Yu Cheng
Keyword(s):  
Social Interactions ◽  
Empirical Research ◽  
Ecological Model ◽  
Specific Time ◽  
Analytic Framework ◽  
Social Time ◽  
Social Actions ◽  
The Social ◽  
Specific Time Point ◽  
Time Point

The purpose of this paper is to outline the “ecology of social time” as an empirical concept of time to bridge the gap between theory and empirical research in the sociology of time. First, this paper proposes that social time could be considered as an institutionalized referential mechanism that enables social interactions to occur at a specific time point by coordinating the social actions of various agents. Examining the condition of temporal coordination and diagnosing its fairness critically may be the tasks involved in the sociology of time. Second, this paper suggests that the ecology of social time is a useful concept for integrating the theses and tasks applied in the sociology of time. Finally, this paper presents an ecological model of social time as a possible framework for subsequent empirical research in the sociology of time.

Assessing Patient State and Efficacy

2018 ◽  
pp. 26-32
Author(s):  
Joseph P. Cravero
Keyword(s):  
Procedural Sedation ◽  
Imaging Procedures ◽  
Specific Time ◽  
Painful Procedure ◽  
Specific Time Point ◽  
Patient State ◽  
A Minor ◽  
Minor Procedure ◽  
Time Point

Pediatric procedural sedation is required for a wide variety of interventions ranging from nonstimulating imaging procedures to painful minor surgeries and other tests. The measurement of how well a given sedation strategy has met the requirements for a procedure is not well codified by simply noting the depth of sedation provided. Patients may be deeply sedated but thrashing about during a painful procedure, and they may be almost awake and perfectly tolerating a minor procedure. Procedural sedation must be measured using a rubric that appreciates the “state” of the patient and qualifies his or her movement, stress, pain, and safety at any specific time point during the procedure. The ability to control these factors and provide an acceptable state for the patient and the proceduralist should be the standard for measuring the quality of sedation provision for children.

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