scholarly journals Time course analysis of the brain transcriptome during transitions between brood care and reproduction in the clonal raider ant

2017 ◽  
Author(s):  
Romain Libbrecht ◽  
Peter R. Oxley ◽  
Daniel J. C. Kronauer
Keyword(s):  
Gene Expression ◽  
Division Of Labor ◽  
Time Course ◽  
Resistance To Change ◽  
Delayed Response ◽  
Multiple Time ◽  
Brood Care ◽  
Insect Societies ◽  
Multiple Time Points ◽  
Care Behavior

AbstractDivision of labor between reproductive queens and non-reproductive workers that perform brood care is the hallmark of insect societies. However, the molecular basis of this fundamental dichotomy remains poorly understood, in part because the caste of an individual cannot typically be experimentally manipulated at the adult stage. Here we take advantage of the unique biology of the clonal raider ant, Ooceraea biroi, where reproduction and brood care behavior can be experimentally manipulated in adults. To study the molecular regulation of reproduction and brood care, we induced transitions between both states, and monitored brain gene expression at multiple time points. We found that introducing larvae that inhibit reproduction and induce brood care behavior caused much faster changes in adult gene expression than removing larvae. The delayed response to the removal of the larval signal prevents untimely activation of reproduction in O. biroi colonies. This resistance to change when removing a signal also prevents premature modifications in many other biological processes. Furthermore, we found that the general patterns of gene expression differ depending on whether ants transition from reproduction to brood care or vice versa, indicating that gene expression changes between phases are cyclic rather than pendular. Our analyses also identify genes with large and early expression changes in one or both transitions. These genes likely play upstream roles in regulating reproduction and behavior, and thus constitute strong candidates for future molecular studies of the evolution and regulation of reproductive division of labor in insect societies.

scholarly journals Temporal gene expression in bovine corpora lutea after treatment with PGF2alpha based on serial biopsies in vivo

Reproduction ◽  
2001 ◽  
pp. 905-913 ◽  
Author(s):  
SJ Tsai ◽  
K Kot ◽  
OJ Ginther ◽  
MC Wiltbank
Keyword(s):  
Gene Expression ◽  
Corpus Luteum ◽  
Time Course ◽  
Regulatory Protein ◽  
Corpora Lutea ◽  
Multiple Time ◽  
Lh Receptor ◽  
Time Points ◽  
Multiple Biopsies ◽  
Fp Receptor

There is growing evidence to indicate that PGF(2alpha)-induced luteolysis involves altered gene expression in the corpus luteum. Concentrations of mRNA encoding nine different gene products were quantified at three time points from corpora lutea in situ. Serial luteal biopsies (2.1-5.5 mg per biopsy) were collected using an ultrasound-guided transvaginal method and mRNA concentrations were quantified with standard curve quantitative competitive RT-PCR. In the first experiment, three luteal biopsies were collected from three heifers and analysed in multiple assays to evaluate the repeatability of the methods. Concentrations of mRNA for glyceraldehyde 3-phosphate dehydrogenase (GAPDH), PGF(2alpha) receptor (FP receptor) and LH receptor were found to be highly repeatable between assays, between multiple biopsies and between animals (coefficients of variation 1.3-17.3%). In the second experiment, heifers on days 9-11 after ovulation were assigned randomly to receive saline only (n = 6), saline with biopsies taken at t = 0, 0.5 and 4.0 h after injection (n = 6), PGF(2alpha) only (n = 6) or PGF(2alpha) with biopsies taken at t = 0, 0.5 and 4.0 h after treatment (n = 7). Biopsy alone did not change corpus luteum diameter, serum progesterone concentrations or days to next ovulation within the saline- or PGF(2alpha)-treated groups. Concentrations of mRNA for steroidogenic acute regulatory protein, FP receptor, 3beta-hydroxysteroid dehydrogenase, cytosolic phospholipase A(2) and LH receptor were decreased at 4.0 h after PGF(2alpha) injection. In contrast, PGF(2alpha) increased mRNA concentrations for prostaglandin G/H synthase-2, monocyte chemoattractant protein-1 and c-fos but the time course differed for induction of these mRNAs. Concentrations of mRNA for GAPDH did not change after PGF(2alpha) treatment. In conclusion, the techniques allowed analysis of multiple, specific mRNAs in an individual corpus luteum at multiple time points without altering subsequent luteal function. Use of these techniques confirmed that luteolysis involves both up- and downregulation of specific mRNA by PGF(2alpha).

Average Formant Trajectories

2019 ◽  
Vol 4 (4) ◽  
pp. 719-732 ◽  
Author(s):  
Steven Sandoval ◽  
Rene L. Utianski ◽  
Heike Lehnert-LeHouillier
Keyword(s):  
Time Course ◽  
American English ◽  
Single Point ◽  
Multiple Time ◽  
Standard American English ◽  
Formant Frequencies ◽  
Automated Method ◽  
Study Support ◽  
Multiple Time Points ◽  
Timit Database

Purpose The use and study of formant frequencies for the description of vowels is commonplace in acoustic phonetics and in attempts to understand results of speech perception studies. Numerous studies have shown that listeners are better able to distinguish vowels when the acoustic parameters are based on spectral information extracted at multiple time points during the duration of the vowel, rather than at a single point in time. The purpose of this study was to validate an automated method for extracting formant trajectories, using information across the time course of production, and subsequently characterize the formant trajectories of vowels using a large, diverse corpus of speech samples. Method Using software tools, we automatically extract the 1st 2 formant frequencies (F1/F2) at 10 equally spaced points over a vowel's duration. Then, we compute the average trajectory for each vowel token. The 1,600 vowel observations in the Hillenbrand database and the more than 50,000 vowel observations in the TIMIT database are analyzed. Results First, we validate the automated method by comparing against the manually obtained values in the Hillenbrand database. Analyses reveal a strong correlation between the automated and manual formant estimates. Then, we use the automated method on the 630 speakers in the TIMIT database to compute average formant trajectories. We noted that phonemes that have close F1 and F2 values at the temporal midpoint often exhibit formant trajectories progressing in different directions, hence highlighting the importance of formant trajectory progression. Conclusions The results of this study support the importance of formant trajectories over single-point measurements for the successful discrimination of vowels. Furthermore, this study provides a baseline for the formant trajectories for men and women across a broad range of dialects of Standard American English.

Gene expression analysis at multiple time-points identifies key genes for nerve regeneration

2016 ◽  
Vol 55 (3) ◽  
pp. 373-383 ◽  
Author(s):  
Bin Pan ◽  
Yi Liu ◽  
Jia-Yin Yan ◽  
Yao Wang ◽  
Xue Yao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nerve Regeneration ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Multiple Time ◽  
Time Points ◽  
Key Genes ◽  
Multiple Time Points

scholarly journals Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells

2017 ◽  
Author(s):  
Mariana Gómez-Schiavon ◽  
Liang-Fu Chen ◽  
Anne E. West ◽  
Nicolas E. Buchler
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Posterior Probability ◽  
Single Cells ◽  
Bayesian Posterior Probability ◽  
Model Parameters ◽  
Multiple Time ◽  
Stochastic Gene Expression ◽  
Time Points ◽  
Multiple Time Points

AbstractSingle-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution on the abundance and localization of nascent and mature transcripts in single cells. Gene expression dynamics are typically inferred by measuring mRNA abundance in small numbers of fixed cells sampled from a population at multiple time-points after induction. The sparse data that arise from the small number of cells obtained using smFISH present a challenge for inferring transcription dynamics. Here, we developed a computational pipeline (BayFish) to infer kinetic parameters of gene expression from smFISH data at multiple time points after induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data. We tested BayFish on smFISH measurements of the neuronal activity inducible gene Npas4 in primary neurons. We showed that a 2-state promoter model can recapitulate Npas4 dynamics after induction and we inferred that the transition rate from the promoter OFF state to the ON state is increased by the stimulus.Author SummaryGene expression can exhibit cell-to-cell variability due to the stochastic nature of biochemical reactions. Single cell assays (e.g. smFISH) directly quantify stochastic gene expression by measuring the number of active promoters and transcripts per cell in a population of cells. The data are distributions and their shape and time-evolution contain critical information on the underlying process of gene expression. Recent work has combined models of stochastic gene expression with maximum likelihood methods to infer kinetic parameters from smFISH distributions. However, these approaches do not provide a probability distribution or likelihood of model parameters inferred from the smFISH data. This information is useful because it indicates which parameters are loosely constrained by the data and suggests follow up experiments. We developed a suite of MATLAB programs (BayFish) that estimate the Bayesian posterior probability of model parameters from smFISH data. The user specifies an underlying model of stochastic gene expression with unknown parameters (θ) and provides smFISH data (Y). BayFish uses a Monte Carlo algorithm to estimate the Bayesian posterior probability P(θ|Y) of model parameters. BayFish is easily modified and can be applied to other models of stochastic gene expression and smFISH data sets.

scholarly journals A novel bioinformatics approach to reveal the role of circadian oscillations in AD development

2020 ◽  
Author(s):  
Zhiwei Ji ◽  
Dazhi Shang ◽  
Pora Kim ◽  
Mengyuan Yang ◽  
Sijia Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Circadian Variation ◽  
Gene Expression Profiles ◽  
Brain Regions ◽  
Multiple Time ◽  
Circadian Genes ◽  
Gene Expression Correlation ◽  
Multiple Time Points

AbstractAltered circadian gene expression may contribute to Alzheimer’s disease (AD) progression. Unfortunately, sampling the central nervous system (CNS) at multiple time points is not feasible. Moreover, there are no AD-related time-series transcriptome datasets available for studying these circadian patterns and their impacts on AD development. In this study, we introduce a novel computational platform, Event-driven Sample Ordering for Circadian Variation Detection (ESOCVD), to reveal rhythmic patterns of gene expression of AD using untimed transcriptome datasets. ESOCVD was applied to 20 untimed gene expression profiles of 16 brain regions from approximately 3000 AD patients in public transcriptome databases. Our analysis revealed five types of circadian alteration patterns in ~2,000 circadian genes in different brain regions of AD patients. Further analyses of additional databases confirmed that our analytical platform can be applied to identify the evolutionary dynamics of circadian variation during the process of AD development. Through the gene expression correlation analysis for our 8 circadian genes identified from AMP-AD MSBB cohorts, we identified stage-specifically enriched biological processes with anticipated context. Gene expression analysis of AD mouse brain tissues further substantiated the predictions of the ESOCVD model. In summary, ESOCVD is highly versatile in bridging circadian research and precision medicine.

scholarly journals In VitroGene Expression Dissected: Chemostat Surgery forMycobacterium tuberculosis

2002 ◽  
Vol 3 (4) ◽  
pp. 345-347 ◽  
Author(s):  
Brian W. James ◽  
Joanna Bacon ◽  
Tobias Hampshire ◽  
Kim Morley ◽  
Philip D. Marsh
Keyword(s):  
Gene Expression ◽  
Culture System ◽  
Time Course ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Multiple Time ◽  
Unique Approach ◽  
Highly Correlated

A unique approach, combining defined and reproduciblein vitromodels with DNA microarrays, has been developed to study environmental modulation of mycobacterial gene expression. The gene expression profiles of samples ofMycobacterium tuberculosis, from independent chemostat cultures grown under defined and reproducible conditions, were found to be highly correlated. This approach is now being used to study the effect of relevant stimuli, such as limited oxygen availability, on mycobacterial gene expression. A modification of the chemostat culture system, enabling largevolume controlled batch culture, has been developed to study starvation survival. Cultures ofM. tuberculosishave been maintained under nutrient-starved conditions for extended periods, with106–107bacilli surviving in a culturable state after 100 days. The design of the culture system has made it possible to control the environment and collect multiple time-course samples to study patterns of gene expression. These studies demonstrate that it is possible to perform long-term studies and obtain reproducible expression data using controlled and definedin vitromodels.

scholarly journals Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Biplabendu Das ◽  
Charissa de Bekker
Keyword(s):  
Gene Expression ◽  
Division Of Labor ◽  
Social Insects ◽  
Regulatory Networks ◽  
Time Course ◽  
Behavioral Plasticity ◽  
Clock Genes ◽  
Daily Rhythms ◽  
Camponotus Floridanus ◽  
Behavioral Castes

Abstract Background Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. Brood-tending nurse ants are usually younger individuals and show “around-the-clock” activity. With age or in the absence of brood, nurses transition into foraging ants that show daily rhythms in activity. Ants can adaptively shift between these behavioral castes and caste-associated chronotypes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity in Camponotus floridanus carpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains. Results We found that nurse brains have three times fewer 24 h oscillating genes than foragers. However, several hundred genes that oscillated every 24 h in forager brains showed robust 8 h oscillations in nurses, including the core clock genes Period and Shaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment and output pathway, including genes said to be involved in regulating insect locomotory behavior. We also found that Vitellogenin, known to regulate division of labor in social insects, showed robust 24 h oscillations in nurse brains but not in foragers. Finally, we found significant overlap between genes differentially expressed between the two ant castes and genes that show ultradian rhythms in daily expression. Conclusion This study provides a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify a putative molecular mechanism underlying plastic timekeeping: several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found in C. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.

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