scholarly journals The molecular basis of socially-mediated phenotypic plasticity in a eusocial paper wasp

2020 ◽  
Author(s):  
Benjamin A. Taylor ◽  
Alessandro Cini ◽  
Christopher D. R. Wyatt ◽  
Max Reuter ◽  
Seirian Sumner
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Paper Wasp ◽  
Strong Response ◽  
Individual Level ◽  
Multiple Phenotypes ◽  
The Individual ◽  
The Relationship

AbstractPhenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Despite this, analyses of the molecular bases of plasticity have been limited by the challenges of linking individual phenotypes with individual-level gene expression profiles, especially in the case of complex social phenotypes. Here, we tackle this challenge by analysing the individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen, a perturbation that induces some individuals to undergo a significant phenotypic shift and become replacement reproductives. Using a machine learning approach, we find a strong response of caste-associated gene expression to queen loss, wherein individuals’ expression profiles become intermediate between queen and worker states. Importantly, this change occurs even in individuals that appear phenotypically unaffected. Part of this response is explained by individual attributes, most prominently age. These results demonstrate that large changes in gene expression may occur in the absence of detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic but not the phenotypic level. Our findings also highlight the complexity of the relationship between gene expression and phenotype, where transcriptomes are neither a direct reflection of the genotype nor a proxy for the molecular underpinnings of the external phenotype.

scholarly journals The molecular basis of socially-mediated phenotypic plasticity in a eusocial paper wasp

2020 ◽  
Author(s):  
Benjamin Taylor ◽  
Alessandro Cini ◽  
Christopher Wyatt ◽  
Max Reuter ◽  
Seirian Sumner
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Paper Wasp ◽  
Strong Response ◽  
Individual Level ◽  
Multiple Phenotypes ◽  
The Individual ◽  
The Relationship

Abstract Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Despite this, analyses of the molecular bases of plasticity have been limited by the challenges of linking individual phenotypes with individual-level gene expression profiles, especially in the case of complex social phenotypes. Here, we tackle this challenge by analysing the individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen, a perturbation that induces some individuals to undergo a significant phenotypic shift and become replacement reproductives. Using a machine learning approach, we find a strong response of caste-associated gene expression to queen loss, wherein individuals’ expression profiles become intermediate between queen and worker states. Importantly, this change occurs even in individuals that appear phenotypically unaffected. Part of this response is explained by individual attributes, most prominently age. These results demonstrate that large changes in gene expression may occur in the absence of detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic but not the phenotypic level. Our findings also highlight the complexity of the relationship between gene expression and phenotype, where transcriptomes are neither a direct reflection of the genotype nor a proxy for the molecular underpinnings of the external phenotype.

scholarly journals The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Benjamin A. Taylor ◽  
Alessandro Cini ◽  
Christopher D. R. Wyatt ◽  
Max Reuter ◽  
Seirian Sumner
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Paper Wasp ◽  
Individual Level ◽  
Multiple Phenotypes ◽  
Machine Learning Approach ◽  
Transcriptomic Level ◽  
The Relationship

AbstractPhenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior.

scholarly journals Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bing He ◽  
Ping Chen ◽  
Sonia Zambrano ◽  
Dina Dabaghie ◽  
Yizhou Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Kidney ◽  
Cell Types ◽  
Model Organisms ◽  
Mural Cell ◽  
Glomerular Cell ◽  
Individual Gene ◽  
The Individual

AbstractMolecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

Relationship Between San-Huang-Xie-Xin-Tang and Its Herbal Components on the Gene Expression Profiles in HepG2 Cells

2008 ◽  
Vol 36 (04) ◽  
pp. 783-797 ◽  
Author(s):  
Wen-Yu Cheng ◽  
Shih-Lu Wu ◽  
Chien-Yun Hsiang ◽  
Chia-Cheng Li ◽  
Tung-Yuan Lai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Major Effect ◽  
Gene Set Enrichment Analysis ◽  
P53 Signaling ◽  
The Relationship ◽  
Herbal Components

Traditional Chinese medicine (TCM) has been used for thousands of years. Most Chinese herbal formulae consist of several herbal components and have been used to treat various diseases. However, the mechanisms of most formulae and the relationship between formulae and their components remain to be elucidated. Here we analyzed the putative mechanism of San-Huang-Xie-Xin-Tang (SHXXT) and defined the relationship between SHXXT and its herbal components by microarray technique. HepG2 cells were treated with SHXXT or its components and the gene expression profiles were analyzed by DNA microarray. Gene set enrichment analysis indicated that SHXXT and its components displayed a unique anti-proliferation pattern via p53 signaling, p53 activated, and DNA damage signaling pathways in HepG2 cells. Network analysis showed that most genes were regulated by one molecule, p53. In addition, hierarchical clustering analysis showed that Rhizoma Coptis shared a similar gene expression profile with SHXXT. These findings may explain why Rhizoma Coptis is the principle herb that exerts the major effect in the herbal formula, SHXXT. Moreover, this is the first report to reveal the relationship between formulae and their herbal components in TCM by microarray and bioinformatics tools.

scholarly journals Artificial Neural Network to Predict Varicocele Impact on Male Fertility through Testicular Endocannabinoid Gene Expression Profiles

2018 ◽  
Vol 2018 ◽  
pp. 1-15
Author(s):  
Davide Perruzza ◽  
Nicola Bernabò ◽  
Cinzia Rapino ◽  
Luca Valbonetti ◽  
Ilaria Falanga ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Artificial Neural Network ◽  
Male Fertility ◽  
Cannabinoid Receptors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Artificial Neural ◽  
The Relationship

The relationship between varicocele and fertility has always been a matter of debate because of the absence of predictive clinical indicators or molecular markers able to define the severity of this disease. Even though accumulated evidence demonstrated that the endocannabinoid system (ECS) plays a central role in male reproductive biology, particularly in the testicular compartment, to date no data point to a role for ECS in the etiopathogenesis of varicocele. Therefore, the present research has been designed to investigate the relationship between testicular ECS gene expression and fertility, using a validated animal model of experimental varicocele (VAR), taking advantage of traditional statistical approaches and artificial neural network (ANN). Experimental induction of VAR led to a clear reduction of spermatogenesis in left testes ranging from a mild (Johnsen score 7: 21%) to a severe (Johnsen score 4: 58%) damage of the germinal epithelium. However, the mean number of new-borns recorded after two sequential matings was quite variable and independent of the Johnsen score. While the gene expression of biosynthetic and degrading enzymes of AEA (NAPE-PLD and FAAH, respectively) and of 2-AG (DAGLα and MAGL, respectively), as well as their binding cannabinoid receptors (CB1 and CB2), did not change between testes and among groups, a significant downregulation of vanilloid (TRPV1) expression was recorded in left testes of VAR rats and positively correlated with animal fertility. Interestingly, an ANN trained by inserting the left and right testicular ECS gene expression profiles (inputs) was able to predict varicocele impact on male fertility in terms of mean number of new-borns delivered (outputs), with a very high accuracy (average prediction error of 1%). The present study provides unprecedented information on testicular ECS gene expression patterns during varicocele, by developing a freely available predictive ANN model that may open new perspectives in the diagnosis of varicocele-associated infertility.

Development and entrainment of the colonic circadian clock during ontogenesis

2014 ◽  
Vol 306 (4) ◽  
pp. G346-G356 ◽  
Author(s):  
Lenka Polidarová ◽  
Lucie Olejníková ◽  
Lucia Paušlyová ◽  
Martin Sládek ◽  
Matúš Soták ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Clock Gene ◽  
Clock Genes ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Perinatal Period ◽  
Circadian Phase ◽  
Clock Gene Expression ◽  
The Individual

Colonic morphology and function change significantly during ontogenesis. In mammals, many colonic physiological functions are temporally controlled by the circadian clock in the colon, which is entrained by the central circadian clock in the suprachiasmatic nuclei (SCN). The aim of this present study was to ascertain when and how the circadian clock in the colon develops during the perinatal period and whether maternal cues and/or the developing pup SCN may influence the ontogenesis of the colonic clock. Daily profiles of clock genes Per1, Per2, Cry1, Cry2, Rev-erbα, Bmal1, and Clock expression in the colon underwent significant modifications since embryonic day 20 (E20) through postnatal days (P) 2, 10, 20, and 30 via changes in the mutual phasing among the individual clock gene expression rhythms, their relative phasing to the light-dark regime, and their amplitudes. An adult-like state was achieved around P20. The foster study revealed that during the prenatal period, the maternal circadian phase may partially modulate development of the colonic clock. Postnatally, the absence and/or presence of rhythmic maternal care affected the phasing of the clock gene expression profiles in pups at P10 and P20. A reversal in the colonic clock phase between P10 and P20 occurred in the absence of rhythmic signals from the pup SCN. The data demonstrate ontogenetic maturation of the colonic clock and stress the importance of prenatal and postnatal maternal rhythmic signals for its development. These data may contribute to the understanding of colonic function-related diseases in newborn children.

scholarly journals Gene expression stasis and plasticity following migration into a foreign environment

2017 ◽  
Author(s):  
Brian K. Lohman ◽  
William E. Stutz ◽  
Daniel I. Bolnick
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profile ◽  
Gasterosteus Aculeatus ◽  
Expression Profiles ◽  
Survival Rates ◽  
Gene Expression Profiles ◽  
Genes Expression ◽  
The Impact ◽  
Fish Performance

AbstractSelection against migrants is key to maintaining genetic differences between populations linked by dispersal. Yet, migrants are not just passively weeded out by selection. Migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. We revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression profiles in stickleback via TagSeq and tested whether migrants between lake and stream habitats exhibited a plastic response to their new environment that allowed them to converge on the expression profile of adapted natives. We report extensive gene expression differences between genetically divergent lake and stream stickleback, despite gene flow. But for many genes, expression was highly plastic. Fish transplanted into the adjoining habitat partially converged on the expression profile typical of their new habitat. This suggests that expression plasticity may soften the impact of migration. Nonetheless, lake and stream fish differed in survival rates and parasite infection rates in our study, implying that expression plasticity is not fast or extensive enough to fully homogenize fish performance.

scholarly journals Putative Multifunctional Signature of Lung Metastases in Dedifferentiated Chondrosarcoma

Sarcoma ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Sergey Malchenko ◽  
Elisabeth A. Seftor ◽  
Yuri Nikolsky ◽  
Susan L. Hasegawa ◽  
Sean Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Metastases ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dedifferentiated Chondrosarcoma ◽  
Lung Lesions ◽  
Metastatic Lung ◽  
The Individual ◽  
First Time ◽  
Aggressive Subtype

Chondrosarcomas are among the most malignant skeletal tumors. Dedifferentiated chondrosarcoma is a highly aggressive subtype of chondrosarcoma, with lung metastases developing within a few months of diagnosis in 90% of patients. In this paper we performed comparative analyses of the transcriptomes of five individual metastatic lung lesions that were surgically resected from a patient with dedifferentiated chondrosarcoma. We document for the first time a high heterogeneity of gene expression profiles among the individual lung metastases. Moreover, we reveal a signature of “multifunctional” genes that are expressed in all metastatic lung lesions. Also, for the first time, we document the occurrence of massive macrophage infiltration in dedifferentiated chondrosarcoma lung metastases.

scholarly journals The Association of Wolbachia on the Gene Expression in Drosophila Adult Testis

2020 ◽  
Author(s):  
Wei-Hao Dou ◽  
Jin-Hua Xiao ◽  
Da-Wei Huang
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Cell Metabolism ◽  
Gene Expression Profiles ◽  
Host Cells ◽  
Membrane Component ◽  
Hydrolysis Process ◽  
New Perspective ◽  
Virus Blocking ◽  
The Relationship

Abstract Background: Wolbachia is a type of intracellular symbiotic bacteria widely distributed in arthropods including most insects and nematodes. These maternally inherited bacteria can regulate the host's reproductive system in various ways for their own vertical transmission. Since the identification of Wolbachia in many insects, the relationship between Wolbachia and host has attracted great interest. Wolbachia must rely on the host cells to survive, and they can also improve the fitness of the host through a variety of ways. However, the molecular basis of interaction between Wolbachia and their host has not been well resolved so far. Results: We performed transcriptome sequencing on testis tissues of adults of Wolbachia-infected and Wolbachia-free Drosophila melanogaster. Comparison of gene expression profiles revealed 471 significantly differentially expressed genes that involved in cell metabolism, cell membrane component correlation and hydrolysis process.Conclusions: Our results show that lipid and carbohydrate metabolism are more active in Wolbachia-infected testis than in Wolbachia free testis. This work strengthens our general understanding of the Wolbachia-host intracellular relationship and may provide a new perspective for Wolbachia-mediated virus-blocking.

scholarly journals A robust method to isolate Drosophila fat body nuclei for transcriptomic analysis

2021 ◽  
Author(s):  
Vanika Gupta ◽  
Brian P. Lazzaro
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Fat Body ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Cell Nuclei ◽  
Preparation Methods ◽  
Physiological Processes ◽  
The Individual

ABSTRACTGene expression profiles are typically described at the level of the tissue or, often in Drosophila, at the level of the whole organism. Collapsing the gene expression of entire tissues into single measures averages over potentially important heterogeneity among the cells that make up that tissue. The advent of single-cell RNA-sequencing technology (sc-RNAseq) allows transcriptomic evaluation of the individual cells that make up a tissue. However, sc-RNAseq requires a high-quality suspension of viable cells or nuclei, and cell dissociation methods that yield healthy cells and nuclei are still lacking for many important tissues. The insect fat body is a polyfunctional tissue responsible for diverse physiological processes and therefore is an important target for sc-RNAseq. The Drosophila adult fat body consists of fragile cells that are difficult to dissociate while maintaining cell viability. As an alternative, we developed a method to isolate single fat body nuclei for RNA-seq. Our isolation method is largely free of mitochondrial contamination and yields higher capture of transcripts per nucleus compared to other nuclei preparation methods. Our method works well for single cell nuclei sequencing and potentially can be implemented for bulk RNA-seq.

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